6-132521257-G-A

Variant names:

• chr6-132521257-G-A
• rs1591811

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 0.654 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.656 AC: 27191 AN: 41456

American (AMR) AF: 0.668 AC: 10216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2427 AN: 3472

East Asian (EAS) AF: 0.869 AC: 4497 AN: 5176

South Asian (SAS) AF: 0.759 AC: 3662 AN: 4822

European-Finnish (FIN) AF: 0.611 AC: 6456 AN: 10558

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42934 AN: 67974

Other (OTH) AF: 0.682 AC: 1441 AN: 2112

Alfa AF: 0.647 Hom.: 136033

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

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