Genetic Variant ENST00000796776.1:n.1309G>A (chr10-94993166-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000796776.1(ENSG00000303732):n.1309G>A 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 0.086 in 152,320 control chromosomes in the GnomAD database, including 719 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 0.086 ( 719 hom., cov: 32)

Consequence

ENSG00000303732
ENST00000796776.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

Publications

4 publications found

Variant links:

Genes affected

ENSG00000303732 (HGNC:):

ENSG00000303732 links:

Genome browser will be placed here

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 (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303732	ENST00000796776.1 link	n.1309G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0861

AC:

13107

AN:

152202

Hom.:

719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0229

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.0973

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0352

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.112

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0860

AC:

13103

AN:

152320

Hom.:

719

Cov.:

AF XY:

0.0850

AC XY:

6331

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0229

AC:

950

AN:

41574

American (AMR)

AF:

0.0971

AC:

1486

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

482

AN:

3468

East Asian (EAS)

AF:

0.000964

AC:

AN:

5188

South Asian (SAS)

AF:

0.0352

AC:

170

AN:

4830

European-Finnish (FIN)

AF:

0.118

AC:

1247

AN:

10612

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8350

AN:

68024

Other (OTH)

AF:

0.111

AC:

235

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

645

1291

1936

2582

3227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0968

Hom.:

101

Bravo

AF:

0.0840

Asia WGS

AF:

0.0150

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.67

(source)

DANN

Benign

0.80

PhyloP100

-1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over