rs1362645

Variant names:

• chr3-179528765-G-A
• rs1362645

Your query was ambiguous. Multiple possible variants found:

• chr3-179528765-G-A
• chr3-179528765-G-C

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 0.676 in 152,150 control chromosomes in the GnomAD database, including 35,400 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 0.68 (35400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.676 AC: 102808 AN: 152032 Hom.: 35341 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.676 AC: 102925 AN: 152150 Hom.: 35400 Cov.: 32 AF XY: 0.681 AC XY: 50642 AN XY: 74360

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.687

Alfa AF: 0.566 Hom.: 2569

Bravo AF: 0.683

Asia WGS AF: 0.834 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362645; hg19: chr3-179246553;