dbSNP rs7584262: ENSG00000226398:n.158-1156G>A (chr2-42023409-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000451514.1(ENSG00000226398):n.158-1156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,980 control chromosomes in the GnomAD database, including 5,917 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 0.26 ( 5917 hom., cov: 32)

Consequence

ENSG00000226398
ENST00000451514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.542

Publications

29 publications found

Variant links:

Genes affected

ENSG00000226398 (HGNC:):

ENSG00000226398 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000226398	ENST00000451514.1 link	n.158-1156G>A	intron_variant	Intron 1 of 2	5
ENSG00000226398	ENST00000777407.1 link	n.236+1737G>A	intron_variant	Intron 1 of 2
ENSG00000226398	ENST00000777408.1 link	n.217+1737G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40207

AN:

151862

Hom.:

5909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.264

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

GnomAD4 genome

AF:

0.265

AC:

40248

AN:

151980

Hom.:

5917

Cov.:

AF XY:

0.264

AC XY:

19614

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.375

AC:

15546

AN:

41424

American (AMR)

AF:

0.182

AC:

2785

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1205

AN:

3468

East Asian (EAS)

AF:

0.00193

AC:

AN:

5172

South Asian (SAS)

AF:

0.224

AC:

1076

AN:

4808

European-Finnish (FIN)

AF:

0.261

AC:

2751

AN:

10542

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.233

AC:

15808

AN:

67978

Other (OTH)

AF:

0.264

AC:

557

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1456

2911

4367

5822

7278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.240

Hom.:

12724

Bravo

AF:

0.263

Asia WGS

AF:

0.129

AC:

452

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.0

(source)

DANN

Benign

0.69

PhyloP100

0.54

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