dbSNP rs2835702: ENSG00000287637:n.188-12555A>G (chr21-37352009-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 ENST00000663813.1(ENSG00000287637):n.188-12555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,170 control chromosomes in the GnomAD database, including 2,693 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 0.18 ( 2693 hom., cov: 32)

Consequence

ENSG00000287637
ENST00000663813.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.195

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287637 (HGNC:):

ENSG00000287637 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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
ENSG00000287637	ENST00000663813.1 link	n.188-12555A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26947

AN:

152052

Hom.:

2683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.177

AC:

26984

AN:

152170

Hom.:

2693

Cov.:

AF XY:

0.181

AC XY:

13501

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.203

AC:

8421

AN:

41514

American (AMR)

AF:

0.175

AC:

2678

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

482

AN:

3472

East Asian (EAS)

AF:

0.367

AC:

1898

AN:

5172

South Asian (SAS)

AF:

0.328

AC:

1584

AN:

4826

European-Finnish (FIN)

AF:

0.164

AC:

1732

AN:

10588

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9655

AN:

67994

Other (OTH)

AF:

0.192

AC:

405

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1125

2249

3374

4498

5623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.164

Hom.:

601

Bravo

AF:

0.180

Asia WGS

AF:

0.357

AC:

1240

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.5

(source)

DANN

Benign

0.88

PhyloP100

0.20

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