6-76617568-C-T

Variant names:

• chr6-76617568-C-T
• rs1563666

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 0.775 in 151,800 control chromosomes in the GnomAD database, including 46,744 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 0.77 (46744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.886 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: 0.775 AC: 117562 AN: 151682 Hom.: 46732 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.775 AC: 117612 AN: 151800 Hom.: 46744 Cov.: 31 AF XY: 0.780 AC XY: 57911 AN XY: 74204

African (AFR) AF: 0.584 AC: 24206 AN: 41414

American (AMR) AF: 0.846 AC: 12887 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3208 AN: 3468

East Asian (EAS) AF: 0.890 AC: 4588 AN: 5154

South Asian (SAS) AF: 0.908 AC: 4375 AN: 4818

European-Finnish (FIN) AF: 0.857 AC: 9033 AN: 10536

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56647 AN: 67860

Other (OTH) AF: 0.800 AC: 1690 AN: 2112

Alfa AF: 0.784 Hom.: 7760

Bravo AF: 0.767

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1563666; hg19: chr6-77327285; COSMIC: COSV69406111;