Genetic Variant ENST00000548520.2:n.2101A>G (chr12-103866509-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000548520.2(ENSG00000293399):n.2101A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 453,684 control chromosomes in the GnomAD database, including 6,639 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2636 hom., cov: 32)

Exomes 𝑓: 0.15 ( 4003 hom. )

Consequence

ENSG00000293399
ENST00000548520.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.77

Publications

7 publications found

Variant links:

Genes affected

ENSG00000293399 (HGNC:):

ENSG00000293399 links:

TTC41P (HGNC:49210): (tetratricopeptide repeat domain 41, pseudogene) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TTC41P links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548520.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC41P	NR_027249.1		n.3142A>G		non_coding_transcript_exon	Exon 11 of 16

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000293399	ENST00000548520.2	TSL:5	n.2101A>G	non_coding_transcript_exon	Exon 6 of 10
ENSG00000293399	ENST00000548527.5	TSL:5	n.240A>G	non_coding_transcript_exon	Exon 3 of 7
TTC41P	ENST00000551270.1	TSL:6	n.2596A>G	non_coding_transcript_exon	Exon 10 of 15

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26371

AN:

151944

Hom.:

2631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.0387

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.166

GnomAD2 exomes

AF:

0.146

AC:

20299

AN:

139154

AF XY:

0.151

show subpopulations

Gnomad AFR exome

AF:

0.263

Gnomad AMR exome

AF:

0.0795

Gnomad ASJ exome

AF:

0.171

Gnomad EAS exome

AF:

0.0418

Gnomad FIN exome

AF:

0.197

Gnomad NFE exome

AF:

0.142

Gnomad OTH exome

AF:

0.137

GnomAD4 exome

AF:

0.153

AC:

46297

AN:

301622

Hom.:

4003

Cov.:

AF XY:

0.159

AC XY:

27198

AN XY:

171354

show subpopulations

African (AFR)

AF:

0.257

AC:

2214

AN:

8600

American (AMR)

AF:

0.0786

AC:

2141

AN:

27232

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

1799

AN:

10744

East Asian (EAS)

AF:

0.0432

AC:

393

AN:

9100

South Asian (SAS)

AF:

0.217

AC:

12937

AN:

59524

European-Finnish (FIN)

AF:

0.193

AC:

2466

AN:

12772

Middle Eastern (MID)

AF:

0.105

AC:

291

AN:

2772

European-Non Finnish (NFE)

AF:

0.140

AC:

21951

AN:

156738

Other (OTH)

AF:

0.149

AC:

2105

AN:

14140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1971

3941

5912

7882

9853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

174

348

522

696

870

<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:

0.174

AC:

26409

AN:

152062

Hom.:

2636

Cov.:

AF XY:

0.175

AC XY:

13022

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.257

AC:

10643

AN:

41452

American (AMR)

AF:

0.111

AC:

1693

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

607

AN:

3466

East Asian (EAS)

AF:

0.0392

AC:

203

AN:

5176

South Asian (SAS)

AF:

0.216

AC:

1041

AN:

4814

European-Finnish (FIN)

AF:

0.198

AC:

2096

AN:

10570

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.140

AC:

9523

AN:

67992

Other (OTH)

AF:

0.165

AC:

348

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1103

2206

3309

4412

5515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.148

Hom.:

3356

Bravo

AF:

0.170

Asia WGS

AF:

0.137

AC:

474

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.028

(source)

DANN

Benign

0.47

PhyloP100

-2.8

Splicing

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