8-6964095-T-C

Variant names:

• chr8-6964095-T-C
• rs2738058

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 0.564 in 152,068 control chromosomes in the GnomAD database, including 24,576 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 0.56 (24576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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: 0.564 AC: 85679 AN: 151950 Hom.: 24546 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.564 AC: 85766 AN: 152068 Hom.: 24576 Cov.: 32 AF XY: 0.561 AC XY: 41716 AN XY: 74314

African (AFR) AF: 0.622 AC: 25778 AN: 41446

American (AMR) AF: 0.513 AC: 7844 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5162

South Asian (SAS) AF: 0.461 AC: 2220 AN: 4812

European-Finnish (FIN) AF: 0.541 AC: 5732 AN: 10586

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38486 AN: 67988

Other (OTH) AF: 0.573 AC: 1211 AN: 2114

Alfa AF: 0.555 Hom.: 18490

Bravo AF: 0.561

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.42
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2738058; hg19: chr8-6821617;