6-112562785-G-A

Variant names:

• chr6-112562785-G-A
• rs6910169

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 0.569 in 151,948 control chromosomes in the GnomAD database, including 25,077 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 0.57 (25077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.569 AC: 86422 AN: 151834 Hom.: 25082 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.569 AC: 86444 AN: 151948 Hom.: 25077 Cov.: 32 AF XY: 0.577 AC XY: 42833 AN XY: 74242

African (AFR) AF: 0.482 AC: 19954 AN: 41426

American (AMR) AF: 0.528 AC: 8053 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2198 AN: 3462

East Asian (EAS) AF: 0.757 AC: 3913 AN: 5170

South Asian (SAS) AF: 0.693 AC: 3342 AN: 4820

European-Finnish (FIN) AF: 0.693 AC: 7319 AN: 10554

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39686 AN: 67966

Other (OTH) AF: 0.559 AC: 1179 AN: 2110

Alfa AF: 0.549 Hom.: 9778

Bravo AF: 0.548

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.64
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs6910169; hg19: chr6-112883987;