dbSNP rs10502459: ENSG00000266573:n.561+71203A>G (chr18-24837937-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000577354.6(ENSG00000266573):n.561+71203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,192 control chromosomes in the GnomAD database, including 797 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 0.066 ( 797 hom., cov: 33)

Consequence

ENSG00000266573
ENST00000577354.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Publications

0 publications found

Variant links:

Genes affected

ENSG00000266573 (HGNC:):

ENSG00000266573 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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
ENSG00000266573	ENST00000577354.6 link	n.561+71203A>G	intron_variant	Intron 3 of 3	4
ENSG00000266573	ENST00000582650.5 link	n.236-89901A>G	intron_variant	Intron 2 of 3	4
ENSG00000266573	ENST00000654065.1 link	n.227-98045A>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0662

AC:

10070

AN:

152074

Hom.:

798

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0164

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00366

Gnomad OTH

AF:

0.0578

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

GnomAD4 genome

AF:

0.0663

AC:

10089

AN:

152192

Hom.:

797

Cov.:

AF XY:

0.0691

AC XY:

5142

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.142

AC:

5902

AN:

41518

American (AMR)

AF:

0.130

AC:

1994

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.000864

AC:

AN:

3472

East Asian (EAS)

AF:

0.221

AC:

1140

AN:

5160

South Asian (SAS)

AF:

0.104

AC:

502

AN:

4812

European-Finnish (FIN)

AF:

0.0164

AC:

174

AN:

10604

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00366

AC:

249

AN:

68010

Other (OTH)

AF:

0.0581

AC:

123

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

425

851

1276

1702

2127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.00881

Hom.:

Bravo

AF:

0.0780

Asia WGS

AF:

0.138

AC:

481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.7

(source)

DANN

Benign

0.68

PhyloP100

1.0

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