chr8-36301253-C-T

Variant names:

• chr8-36301253-C-T
• rs670603

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 0.58 in 151,930 control chromosomes in the GnomAD database, including 26,802 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 0.58 (26802 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 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: 0.580 AC: 88085 AN: 151812 Hom.: 26816 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.580 AC: 88065 AN: 151930 Hom.: 26802 Cov.: 31 AF XY: 0.577 AC XY: 42850 AN XY: 74248

African (AFR) AF: 0.410 AC: 16968 AN: 41418

American (AMR) AF: 0.531 AC: 8088 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1764 AN: 5142

South Asian (SAS) AF: 0.526 AC: 2528 AN: 4810

European-Finnish (FIN) AF: 0.743 AC: 7857 AN: 10580

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46410 AN: 67962

Other (OTH) AF: 0.551 AC: 1163 AN: 2110

Alfa AF: 0.642 Hom.: 21253

Bravo AF: 0.556

Asia WGS AF: 0.431 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.35
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs670603; hg19: chr8-36158771; COSMIC: COSV56012388;