dbSNP rs11591710: ENSG00000289744:n.274-10218T>G (chr10-103927874-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000698239.1(ENSG00000289744):n.274-10218T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,136 control chromosomes in the GnomAD database, including 2,352 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 0.16 ( 2352 hom., cov: 32)

Consequence

ENSG00000289744
ENST00000698239.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.650

Publications

20 publications found

Variant links:

Genes affected

ENSG00000289744 (HGNC:):

ENSG00000289744 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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
ENSG00000289744	ENST00000698239.1 link	n.274-10218T>G		intron_variant	Intron 2 of 11
ENSG00000289744	ENST00000698240.1 link	n.389-10218T>G		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24412

AN:

152018

Hom.:

2336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.167

Gnomad EAS

AF:

0.0127

Gnomad SAS

AF:

0.0901

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.161

AC:

24468

AN:

152136

Hom.:

2352

Cov.:

AF XY:

0.156

AC XY:

11632

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.260

AC:

10789

AN:

41446

American (AMR)

AF:

0.109

AC:

1659

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

580

AN:

3470

East Asian (EAS)

AF:

0.0131

AC:

AN:

5188

South Asian (SAS)

AF:

0.0891

AC:

430

AN:

4824

European-Finnish (FIN)

AF:

0.113

AC:

1193

AN:

10598

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.137

AC:

9330

AN:

68006

Other (OTH)

AF:

0.158

AC:

334

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

998

1996

2994

3992

4990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.149

Hom.:

231

Bravo

AF:

0.164

Asia WGS

AF:

0.112

AC:

388

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.1

(source)

DANN

Benign

0.43

PhyloP100

0.65

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