dbSNP rs7758736: ENSG00000302653:n.13G>A (chr6-32790617-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000788564.1(ENSG00000302653):n.13G>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 0.14 in 152,104 control chromosomes in the GnomAD database, including 1,641 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 0.14 ( 1641 hom., cov: 31)

Consequence

ENSG00000302653
ENST00000788564.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

39 publications found

Variant links:

Genes affected

ENSG00000302653 (HGNC:):

ENSG00000302653 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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
ENSG00000302653	ENST00000788564.1 link	n.13G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21322

AN:

151986

Hom.:

1640

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.0716

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.0231

Gnomad SAS

AF:

0.0964

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.143

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

GnomAD4 genome

AF:

0.140

AC:

21319

AN:

152104

Hom.:

1641

Cov.:

AF XY:

0.138

AC XY:

10263

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.102

AC:

4231

AN:

41496

American (AMR)

AF:

0.129

AC:

1965

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

553

AN:

3470

East Asian (EAS)

AF:

0.0231

AC:

120

AN:

5184

South Asian (SAS)

AF:

0.0963

AC:

464

AN:

4820

European-Finnish (FIN)

AF:

0.171

AC:

1808

AN:

10584

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11767

AN:

67952

Other (OTH)

AF:

0.141

AC:

298

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

920

1840

2760

3680

4600

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.162

Hom.:

8056

Bravo

AF:

0.133

Asia WGS

AF:

0.0680

AC:

243

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.59

(source)

DANN

Benign

0.74

PhyloP100

-2.0

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