Genetic Variant NM_005422.4:c.4422C>T (chr11-121157957-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_005422.4(TECTA):c.4422C>T(p.Asn1474Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 1,613,760 control chromosomes in the GnomAD database, including 852 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.022 ( 59 hom., cov: 33)

Exomes 𝑓: 0.030 ( 793 hom. )

Consequence

TECTA
NM_005422.4 synonymous

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:6

Conservation

PhyloP100: -0.402

Publications

3 publications found

Variant links:

Genes affected

TECTA (HGNC:11720): (tectorin alpha) The tectorial membrane is an extracellular matrix of the inner ear that contacts the stereocilia bundles of specialized sensory hair cells. Sound induces movement of these hair cells relative to the tectorial membrane, deflects the stereocilia, and leads to fluctuations in hair-cell membrane potential, transducing sound into electrical signals. Alpha-tectorin is one of the major noncollagenous components of the tectorial membrane. Mutations in the TECTA gene have been shown to be responsible for autosomal dominant nonsyndromic hearing impairment and a recessive form of sensorineural pre-lingual non-syndromic deafness. [provided by RefSeq, Jul 2008]

TECTA links:

TBCEL-TECTA (HGNC:54857): (TBCEL-TECTA readthrough) Predicted to enable alpha-tubulin binding activity. Predicted to be involved in microtubule cytoskeleton organization; post-chaperonin tubulin folding pathway; and tubulin complex assembly. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TBCEL-TECTA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 11-121157957-C-T is Benign according to our data. Variant chr11-121157957-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 45331.

BP7

Synonymous conserved (PhyloP=-0.402 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0215 (3279/152376) while in subpopulation NFE AF = 0.0349 (2372/68036). AF 95% confidence interval is 0.0337. There are 59 homozygotes in GnomAd4. There are 1454 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 59 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005422.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TECTA	NM_005422.4	MANE Select	c.4422C>T	p.Asn1474Asn	synonymous	Exon 14 of 24	NP_005413.2	O75443
	TBCEL-TECTA	NM_001378761.1		c.5379C>T	p.Asn1793Asn	synonymous	Exon 20 of 30	NP_001365690.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TECTA	ENST00000392793.6	TSL:5 MANE Select	c.4422C>T	p.Asn1474Asn	synonymous	Exon 14 of 24	ENSP00000376543.1	O75443
TECTA	ENST00000264037.2	TSL:1	c.4422C>T	p.Asn1474Asn	synonymous	Exon 13 of 23	ENSP00000264037.2	O75443
TECTA	ENST00000642222.1		c.4422C>T	p.Asn1474Asn	synonymous	Exon 14 of 24	ENSP00000493855.1	A0A2R8YDL0

Frequencies

GnomAD3 genomes

AF:

0.0215

AC:

3281

AN:

152258

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00562

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0141

Gnomad ASJ

AF:

0.0660

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.0133

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0349

Gnomad OTH

AF:

0.0205

GnomAD2 exomes

AF:

0.0214

AC:

5350

AN:

250300

AF XY:

0.0214

show subpopulations

Gnomad AFR exome

AF:

0.00502

Gnomad AMR exome

AF:

0.0103

Gnomad ASJ exome

AF:

0.0703

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.0139

Gnomad NFE exome

AF:

0.0314

Gnomad OTH exome

AF:

0.0250

GnomAD4 exome

AF:

0.0301

AC:

43964

AN:

1461384

Hom.:

793

Cov.:

AF XY:

0.0295

AC XY:

21422

AN XY:

727048

show subpopulations

African (AFR)

AF:

0.00427

AC:

143

AN:

33478

American (AMR)

AF:

0.0110

AC:

494

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.0685

AC:

1788

AN:

26118

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39698

South Asian (SAS)

AF:

0.00648

AC:

559

AN:

86250

European-Finnish (FIN)

AF:

0.0165

AC:

873

AN:

53030

Middle Eastern (MID)

AF:

0.00728

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0345

AC:

38396

AN:

1111950

Other (OTH)

AF:

0.0276

AC:

1667

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

3127

6254

9381

12508

15635

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1452

2904

4356

5808

7260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0215

AC:

3279

AN:

152376

Hom.:

Cov.:

AF XY:

0.0195

AC XY:

1454

AN XY:

74518

show subpopulations

African (AFR)

AF:

0.00563

AC:

234

AN:

41594

American (AMR)

AF:

0.0140

AC:

215

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0660

AC:

229

AN:

3470

East Asian (EAS)

AF:

0.000579

AC:

AN:

5184

South Asian (SAS)

AF:

0.00807

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0133

AC:

141

AN:

10630

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0349

AC:

2372

AN:

68036

Other (OTH)

AF:

0.0203

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

170

339

509

678

848

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0291

Hom.:

154

Bravo

AF:

0.0207

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0302

EpiControl

AF:

0.0273

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (3)

not provided (2)

Autosomal dominant nonsyndromic hearing loss 12 (1)

Autosomal recessive nonsyndromic hearing loss 21 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

9.9

(source)

DANN

Benign

0.82

PhyloP100

-0.40

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over