dbSNP rs585070: ENSG00000287231:n.133-79024A>G (chr10-111868128-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 ENST00000656217.1(ENSG00000287231):n.133-79024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,034 control chromosomes in the GnomAD database, including 15,371 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 0.44 ( 15371 hom., cov: 33)

Consequence

ENSG00000287231
ENST00000656217.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.740

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287231 (HGNC:):

ENSG00000287231 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 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
ENSG00000287231	ENST00000656217.1 link	n.133-79024A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

66138

AN:

151916

Hom.:

15376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.445

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

GnomAD4 genome

AF:

0.435

AC:

66148

AN:

152034

Hom.:

15371

Cov.:

AF XY:

0.434

AC XY:

32271

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.283

AC:

11719

AN:

41470

American (AMR)

AF:

0.363

AC:

5543

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.446

AC:

1548

AN:

3468

East Asian (EAS)

AF:

0.327

AC:

1691

AN:

5166

South Asian (SAS)

AF:

0.430

AC:

2074

AN:

4820

European-Finnish (FIN)

AF:

0.559

AC:

5901

AN:

10564

Middle Eastern (MID)

AF:

0.493

AC:

144

AN:

292

European-Non Finnish (NFE)

AF:

0.531

AC:

36101

AN:

67956

Other (OTH)

AF:

0.445

AC:

938

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1846

3692

5537

7383

9229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

620

1240

1860

2480

3100

<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:

0.489

Hom.:

50682

Bravo

AF:

0.414

Asia WGS

AF:

0.365

AC:

1270

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.0

(source)

DANN

Benign

0.76

PhyloP100

0.74

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