dbSNP rs4972593: ENSG00000270460:n.391+64787T>A (chr2-173598126-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 ENST00000737367.1(ENSG00000270460):n.391+64787T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,022 control chromosomes in the GnomAD database, including 3,554 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 0.20 ( 3554 hom., cov: 32)

Consequence

ENSG00000270460
ENST00000737367.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166

Publications

21 publications found

Variant links:

Genes affected

ENSG00000270460 (HGNC:):

ENSG00000270460 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) 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
ENSG00000270460	ENST00000737367.1 link	n.391+64787T>A	intron_variant	Intron 2 of 3
ENSG00000270460	ENST00000737368.1 link	n.518+64787T>A	intron_variant	Intron 1 of 2
ENSG00000270460	ENST00000737369.1 link	n.503+64787T>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

30400

AN:

151904

Hom.:

3551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.199

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

GnomAD4 genome

AF:

0.200

AC:

30423

AN:

152022

Hom.:

3554

Cov.:

AF XY:

0.198

AC XY:

14687

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.306

AC:

12690

AN:

41462

American (AMR)

AF:

0.124

AC:

1898

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

791

AN:

3466

East Asian (EAS)

AF:

0.200

AC:

1033

AN:

5176

South Asian (SAS)

AF:

0.355

AC:

1714

AN:

4822

European-Finnish (FIN)

AF:

0.101

AC:

1070

AN:

10598

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10598

AN:

67908

Other (OTH)

AF:

0.199

AC:

420

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1205

2411

3616

4822

6027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.180

Hom.:

318

Bravo

AF:

0.201

Asia WGS

AF:

0.287

AC:

997

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

(source)

DANN

Benign

0.67

PhyloP100

0.17

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