chr6-32603062-A-G

Variant names:

• chr6-32603062-A-G
• rs9270856

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 0.744 in 151,436 control chromosomes in the GnomAD database, including 42,111 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 0.74 (42111 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.744 AC: 112638 AN: 151320 Hom.: 42077 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.744 AC: 112722 AN: 151436 Hom.: 42111 Cov.: 30 AF XY: 0.742 AC XY: 54862 AN XY: 73978

African (AFR) AF: 0.767 AC: 31637 AN: 41232

American (AMR) AF: 0.787 AC: 11990 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2724 AN: 3464

East Asian (EAS) AF: 0.804 AC: 4142 AN: 5154

South Asian (SAS) AF: 0.728 AC: 3496 AN: 4800

European-Finnish (FIN) AF: 0.655 AC: 6869 AN: 10480

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49377 AN: 67770

Other (OTH) AF: 0.770 AC: 1617 AN: 2100

Alfa AF: 0.738 Hom.: 56612

Bravo AF: 0.759

Asia WGS AF: 0.710 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs9270856; hg19: chr6-32570839;