dbSNP rs1324467: ENSG00000290538:n.273-7150T>A (chr9-36005887-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 ENST00000647905.1(ENSG00000290538):n.273-7150T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,096 control chromosomes in the GnomAD database, including 943 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 0.084 ( 943 hom., cov: 32)

Consequence

ENSG00000290538
ENST00000647905.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Publications

1 publications found

Variant links:

Genes affected

ENSG00000290538 (HGNC:):

ENSG00000290538 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000290538	ENST00000647905.1 link	n.273-7150T>A	intron_variant	Intron 2 of 2
ENSG00000290538	ENST00000806593.1 link	n.57-7150T>A	intron_variant	Intron 1 of 1
ENSG00000290538	ENST00000806594.1 link	n.330-7150T>A	intron_variant	Intron 1 of 1
ENSG00000290538	ENST00000806595.1 link	n.298-7050T>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0837

AC:

12727

AN:

151978

Hom.:

935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0261

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0698

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.0754

Gnomad OTH

AF:

0.101

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

GnomAD4 genome

AF:

0.0838

AC:

12746

AN:

152096

Hom.:

943

Cov.:

AF XY:

0.0883

AC XY:

6568

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0263

AC:

1091

AN:

41482

American (AMR)

AF:

0.106

AC:

1624

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0698

AC:

242

AN:

3466

East Asian (EAS)

AF:

0.403

AC:

2083

AN:

5168

South Asian (SAS)

AF:

0.169

AC:

815

AN:

4818

European-Finnish (FIN)

AF:

0.131

AC:

1387

AN:

10568

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0754

AC:

5125

AN:

68000

Other (OTH)

AF:

0.109

AC:

229

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

560

1121

1681

2242

2802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0776

Hom.:

Bravo

AF:

0.0801

Asia WGS

AF:

0.270

AC:

942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

0.014

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