rs1879976

Variant names:

• chr3-148625730-G-A
• rs1879976

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 0.526 in 152,008 control chromosomes in the GnomAD database, including 21,212 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 0.53 (21212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

ACMG classification

Verdict is Benign. Variant got -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 = 0.636 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: 0.526 AC: 79920 AN: 151890 Hom.: 21180 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.526 AC: 79998 AN: 152008 Hom.: 21212 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74302

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.511

Alfa AF: 0.496 Hom.: 30911

Bravo AF: 0.527

Asia WGS AF: 0.615 AC: 2136 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879976; hg19: chr3-148343517;