rs1348979

Variant names:

• chr3-26986006-G-C
• rs1348979

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 0.312 in 152,018 control chromosomes in the GnomAD database, including 7,754 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 0.31 (7754 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 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: 0.312 AC: 47350 AN: 151900 Hom.: 7742 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.312 AC: 47386 AN: 152018 Hom.: 7754 Cov.: 32 AF XY: 0.304 AC XY: 22587 AN XY: 74300

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.336

Alfa AF: 0.326 Hom.: 1020

Bravo AF: 0.318

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348979; hg19: chr3-27027497;