chr6-85251291-C-T

Variant names:

• chr6-85251291-C-T
• rs1570108

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 0.724 in 152,032 control chromosomes in the GnomAD database, including 40,235 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 0.72 (40235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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: 0.723 AC: 109906 AN: 151914 Hom.: 40184 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.724 AC: 110013 AN: 152032 Hom.: 40235 Cov.: 32 AF XY: 0.723 AC XY: 53676 AN XY: 74278

African (AFR) AF: 0.805 AC: 33422 AN: 41506

American (AMR) AF: 0.804 AC: 12272 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4873 AN: 5166

South Asian (SAS) AF: 0.628 AC: 3033 AN: 4828

European-Finnish (FIN) AF: 0.616 AC: 6503 AN: 10550

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45098 AN: 67928

Other (OTH) AF: 0.736 AC: 1554 AN: 2112

Alfa AF: 0.694 Hom.: 4587

Bravo AF: 0.746

Asia WGS AF: 0.769 AC: 2673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Benign	0.37
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs1570108; hg19: chr6-85961009; COSMIC: COSV69410987;