Variant chr11-121102565-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_005422.4(TECTA):c.-1-100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 880,136 control chromosomes in the GnomAD database, including 135 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0077 ( 6 hom., cov: 32)

Exomes 𝑓: 0.012 ( 129 hom. )

Consequence

TECTA
NM_005422.4 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.181

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:):

TBCEL-TECTA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 11-121102565-C-T is Benign according to our data. Variant chr11-121102565-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1209193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00774 (1179/152272) while in subpopulation SAS AF= 0.033 (159/4824). AF 95% confidence interval is 0.0288. There are 6 homozygotes in gnomad4. There are 586 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TECTA	NM_005422.4 linkuse as main transcript	c.-1-100C>T		intron_variant		ENST00000392793.6	NP_005413.2
TBCEL-TECTA	NM_001378761.1 linkuse as main transcript	c.957-100C>T		intron_variant			NP_001365690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TECTA	ENST00000392793.6 linkuse as main transcript	c.-1-100C>T		intron_variant		5	NM_005422.4	ENSP00000376543	P4
TECTA	ENST00000642222.1 linkuse as main transcript	c.-1-100C>T		intron_variant				ENSP00000493855	A1

Frequencies

GnomAD3 genomes

AF:

0.00778

AC:

1184

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00576

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0333

Gnomad FIN

AF:

0.00330

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.0124

GnomAD4 exome

AF:

0.0122

AC:

8862

AN:

727864

Hom.:

129

AF XY:

0.0136

AC XY:

5306

AN XY:

388812

show subpopulations

Gnomad4 AFR exome

AF:

0.00126

Gnomad4 AMR exome

AF:

0.00506

Gnomad4 ASJ exome

AF:

0.0181

Gnomad4 EAS exome

AF:

0.0000279

Gnomad4 SAS exome

AF:

0.0343

Gnomad4 FIN exome

AF:

0.00457

Gnomad4 NFE exome

AF:

0.0113

Gnomad4 OTH exome

AF:

0.0120

GnomAD4 genome

AF:

0.00774

AC:

1179

AN:

152272

Hom.:

Cov.:

AF XY:

0.00787

AC XY:

586

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00173

Gnomad4 AMR

AF:

0.00562

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0330

Gnomad4 FIN

AF:

0.00330

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00938

Hom.:

Bravo

AF:

0.00711

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 25, 2019	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

6.4

DANN

Benign

0.67

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over