15-74764862-G-T

Variant names:

• chr15-74764862-G-T
• rs4886406

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 0.683 in 152,014 control chromosomes in the GnomAD database, including 35,676 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 0.68 (35676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 22 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 (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.683 AC: 103704 AN: 151896 Hom.: 35643 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.683 AC: 103788 AN: 152014 Hom.: 35676 Cov.: 31 AF XY: 0.680 AC XY: 50510 AN XY: 74316

African (AFR) AF: 0.615 AC: 25460 AN: 41426

American (AMR) AF: 0.711 AC: 10873 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2515 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3299 AN: 5166

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4826

European-Finnish (FIN) AF: 0.719 AC: 7597 AN: 10564

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48943 AN: 67964

Other (OTH) AF: 0.677 AC: 1429 AN: 2110

Alfa AF: 0.704 Hom.: 61454

Bravo AF: 0.683

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.42
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4886406; hg19: chr15-75057203;