rs1369276

chr3-164442850-C-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 0.505 in 151,514 control chromosomes in the GnomAD database, including 19,670 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 0.51 (19670 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.505 AC: 76484 AN: 151396 Hom.: 19639 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.505 AC: 76566 AN: 151514 Hom.: 19670 Cov.: 31 AF XY: 0.504 AC XY: 37315 AN XY: 74026

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.490

Alfa AF: 0.495 Hom.: 3088

Bravo AF: 0.516

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.047
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369276; hg19: chr3-164160638;