rs1504232

Variant names:

• chr11-38717133-G-A
• rs1504232

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.941

Alfa AF: 0.944 Hom.: 9699

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504232; hg19: chr11-38738683;