5-110047518-T-C

Variant names:

• chr5-110047518-T-C
• rs2966762

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 0.571 in 151,934 control chromosomes in the GnomAD database, including 25,508 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 0.57 (25508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.571 AC: 86636 AN: 151814 Hom.: 25502 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.571 AC: 86686 AN: 151934 Hom.: 25508 Cov.: 32 AF XY: 0.579 AC XY: 42996 AN XY: 74232

African (AFR) AF: 0.426 AC: 17649 AN: 41442

American (AMR) AF: 0.646 AC: 9848 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2034 AN: 3466

East Asian (EAS) AF: 0.792 AC: 4074 AN: 5146

South Asian (SAS) AF: 0.714 AC: 3439 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6635 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41102 AN: 67944

Other (OTH) AF: 0.581 AC: 1224 AN: 2108

Alfa AF: 0.590 Hom.: 79036

Bravo AF: 0.562

Asia WGS AF: 0.695 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2966762; hg19: chr5-109383219;