dbSNP rs10496098: ENSG00000228541:n.332+29001T>A (chr2-62530324-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000807713.1(ENSG00000228541):n.332+29001T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0992 in 152,228 control chromosomes in the GnomAD database, including 891 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 0.099 ( 891 hom., cov: 33)

Consequence

ENSG00000228541
ENST00000807713.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00600

Publications

0 publications found

Variant links:

Genes affected

ENSG00000228541 (HGNC:):

ENSG00000228541 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228541	ENST00000807713.1 link	n.332+29001T>A	intron_variant	Intron 2 of 4
ENSG00000228541	ENST00000807714.1 link	n.229-24798T>A	intron_variant	Intron 2 of 3
ENSG00000228541	ENST00000807715.1 link	n.242+29001T>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0993

AC:

15097

AN:

152110

Hom.:

894

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0518

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.0952

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.0992

AC:

15097

AN:

152228

Hom.:

891

Cov.:

AF XY:

0.0983

AC XY:

7316

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0518

AC:

2153

AN:

41538

American (AMR)

AF:

0.0951

AC:

1455

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

414

AN:

3472

East Asian (EAS)

AF:

0.000579

AC:

AN:

5182

South Asian (SAS)

AF:

0.0439

AC:

212

AN:

4824

European-Finnish (FIN)

AF:

0.131

AC:

1381

AN:

10582

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9041

AN:

68012

Other (OTH)

AF:

0.115

AC:

243

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

710

1420

2129

2839

3549

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.116

Hom.:

136

Bravo

AF:

0.0950

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

5.3

(source)

DANN

Benign

0.72

PhyloP100

-0.0060

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