6-61253680-C-T

Variant names:

• chr6-61253680-C-T
• rs840061

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 0.832 in 152,068 control chromosomes in the GnomAD database, including 52,940 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 0.83 (52940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 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: 0.832 AC: 126489 AN: 151950 Hom.: 52901 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.832 AC: 126583 AN: 152068 Hom.: 52940 Cov.: 33 AF XY: 0.827 AC XY: 61445 AN XY: 74294

African (AFR) AF: 0.779 AC: 32331 AN: 41500

American (AMR) AF: 0.816 AC: 12456 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2733 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3633 AN: 5150

South Asian (SAS) AF: 0.778 AC: 3745 AN: 4814

European-Finnish (FIN) AF: 0.866 AC: 9174 AN: 10590

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59782 AN: 67966

Other (OTH) AF: 0.817 AC: 1728 AN: 2114

Alfa AF: 0.862 Hom.: 12787

Bravo AF: 0.827

Asia WGS AF: 0.726 AC: 2525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.58
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs840061; hg19: chr6-61984034;