dbSNP rs4711652: ENSG00000293636:n.631-1897C>T (chr6-40885000-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 ENST00000716631.1(ENSG00000293636):n.631-1897C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,020 control chromosomes in the GnomAD database, including 19,718 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 0.50 ( 19718 hom., cov: 32)

Consequence

ENSG00000293636
ENST00000716631.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Publications

3 publications found

Variant links:

Genes affected

ENSG00000293636 (HGNC:):

ENSG00000293636 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929555	NR_110873.1 link	n.595-1897C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293636	ENST00000716631.1 link	n.631-1897C>T	intron_variant	Intron 5 of 8
ENSG00000293636	ENST00000716633.1 link	n.838-1897C>T	intron_variant	Intron 6 of 7
ENSG00000293636	ENST00000740548.1 link	n.585-1897C>T	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.498

AC:

75579

AN:

151902

Hom.:

19711

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.840

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.586

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.521

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

GnomAD4 genome

AF:

0.497

AC:

75605

AN:

152020

Hom.:

19718

Cov.:

AF XY:

0.501

AC XY:

37201

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.343

AC:

14219

AN:

41436

American (AMR)

AF:

0.492

AC:

7517

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.550

AC:

1911

AN:

3472

East Asian (EAS)

AF:

0.683

AC:

3535

AN:

5172

South Asian (SAS)

AF:

0.459

AC:

2208

AN:

4806

European-Finnish (FIN)

AF:

0.586

AC:

6188

AN:

10560

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.559

AC:

37963

AN:

67966

Other (OTH)

AF:

0.524

AC:

1107

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1878

3755

5633

7510

9388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.542

Hom.:

93635

Bravo

AF:

0.489

Asia WGS

AF:

0.523

AC:

1819

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.7

(source)

DANN

Benign

0.73

PhyloP100

0.34

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