dbSNP rs10508755: ENSG00000289616:n.538-5896G>A (chr10-29957351-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 ENST00000839508.1(ENSG00000289616):n.538-5896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,068 control chromosomes in the GnomAD database, including 2,554 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 0.11 ( 2554 hom., cov: 33)

Consequence

ENSG00000289616
ENST00000839508.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60

Publications

1 publications found

Variant links:

Genes affected

ENSG00000289616 (HGNC:):

ENSG00000289616 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289616	ENST00000839508.1 link	n.538-5896G>A	intron_variant	Intron 1 of 2
ENSG00000309221	ENST00000839588.1 link	n.409+2186C>T	intron_variant	Intron 1 of 2
ENSG00000309221	ENST00000839589.1 link	n.409+2186C>T	intron_variant	Intron 1 of 2
ENSG00000309221	ENST00000839590.1 link	n.267+2698C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16172

AN:

151950

Hom.:

2537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0442

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.0688

Gnomad FIN

AF:

0.000850

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.00847

Gnomad OTH

AF:

0.0845

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

GnomAD4 genome

AF:

0.107

AC:

16227

AN:

152068

Hom.:

2554

Cov.:

AF XY:

0.104

AC XY:

7766

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.345

AC:

14305

AN:

41434

American (AMR)

AF:

0.0443

AC:

676

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3472

East Asian (EAS)

AF:

0.00271

AC:

AN:

5172

South Asian (SAS)

AF:

0.0680

AC:

327

AN:

4810

European-Finnish (FIN)

AF:

0.000850

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00848

AC:

577

AN:

68010

Other (OTH)

AF:

0.0837

AC:

176

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

553

1107

1660

2214

2767

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:

0.0168

Hom.:

Bravo

AF:

0.120

Asia WGS

AF:

0.0480

AC:

167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.98

(source)

DANN

Benign

0.59

PhyloP100

-1.6

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