rs1504232

Variant names:

• chr11-38717133-G-A
• rs1504232

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.912 in 152,022 control chromosomes in the GnomAD database, including 64,225 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 0.91 (64225 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138563 AN: 151902 Hom.: 64207 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.912 AC: 138626 AN: 152022 Hom.: 64225 Cov.: 31 AF XY: 0.913 AC XY: 67792 AN XY: 74272

African (AFR) AF: 0.735 AC: 30478 AN: 41490

American (AMR) AF: 0.957 AC: 14576 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3390 AN: 3470

East Asian (EAS) AF: 0.895 AC: 4605 AN: 5146

South Asian (SAS) AF: 0.923 AC: 4452 AN: 4824

European-Finnish (FIN) AF: 0.988 AC: 10477 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67471 AN: 67928

Other (OTH) AF: 0.941 AC: 1988 AN: 2112

Alfa AF: 0.937 Hom.: 9905

Bravo AF: 0.903

Asia WGS AF: 0.909 AC: 3162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1504232; hg19: chr11-38738683;