rs1879976

chr3-148625730-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;