rs843360

Variant names:

• chr3-184148012-T-A
• rs843360

Your query was ambiguous. Multiple possible variants found:

• chr3-184148012-T-A
• chr3-184148012-T-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 0.467 in 151,820 control chromosomes in the GnomAD database, including 16,788 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 0.47 (16788 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 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: 0.467 AC: 70864 AN: 151702 Hom.: 16770 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.467 AC: 70921 AN: 151820 Hom.: 16788 Cov.: 31 AF XY: 0.468 AC XY: 34733 AN XY: 74174

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.455

Alfa AF: 0.280 Hom.: 620

Bravo AF: 0.462

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs843360; hg19: chr3-183865800;