8-24958616-C-T

Variant names:

• chr8-24958616-C-T
• rs2976437

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 0.547 in 151,950 control chromosomes in the GnomAD database, including 24,457 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 0.55 (24457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.654 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: 0.547 AC: 83094 AN: 151832 Hom.: 24447 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.547 AC: 83133 AN: 151950 Hom.: 24457 Cov.: 31 AF XY: 0.551 AC XY: 40917 AN XY: 74254

African (AFR) AF: 0.317 AC: 13120 AN: 41452

American (AMR) AF: 0.665 AC: 10147 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3018 AN: 5148

South Asian (SAS) AF: 0.672 AC: 3224 AN: 4800

European-Finnish (FIN) AF: 0.610 AC: 6435 AN: 10546

Middle Eastern (MID) AF: 0.559 AC: 162 AN: 290

European-Non Finnish (NFE) AF: 0.640 AC: 43495 AN: 67956

Other (OTH) AF: 0.548 AC: 1158 AN: 2112

Alfa AF: 0.577 Hom.: 9649

Bravo AF: 0.541

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.64
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2976437; hg19: chr8-24816130;