rs974379

Variant names:

• chr15-33212866-C-A
• rs974379

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.777 in 151,958 control chromosomes in the GnomAD database, including 49,714 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 0.78 (49714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 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: 0.777 AC: 118026 AN: 151840 Hom.: 49706 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.777 AC: 118069 AN: 151958 Hom.: 49714 Cov.: 31 AF XY: 0.782 AC XY: 58110 AN XY: 74294

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.796

Alfa AF: 0.889 Hom.: 83451

Bravo AF: 0.752

Asia WGS AF: 0.831 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs974379; hg19: chr15-33505067;