rs1504232

chr11-38717133-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;