rs1591811

chr6-132521257-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 0.654 in 152,060 control chromosomes in the GnomAD database, including 32,851 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 0.65 (32851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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: 0.654 AC: 99386 AN: 151942 Hom.: 32837 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.654 AC: 99450 AN: 152060 Hom.: 32851 Cov.: 32 AF XY: 0.657 AC XY: 48867 AN XY: 74328

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.682

Alfa AF: 0.646 Hom.: 64305

Bravo AF: 0.658

Asia WGS AF: 0.811 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1591811; hg19: chr6-132842396; COSMIC: COSV70418601;