3-183917091-T-C

Variant names:

• chr3-183917091-T-C
• rs1533682

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 0.63 in 152,010 control chromosomes in the GnomAD database, including 31,068 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 0.63 (31068 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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 (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.629 AC: 95596 AN: 151892 Hom.: 31015 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.630 AC: 95705 AN: 152010 Hom.: 31068 Cov.: 32 AF XY: 0.624 AC XY: 46367 AN XY: 74324

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.640

Alfa AF: 0.568 Hom.: 32841

Bravo AF: 0.642

Asia WGS AF: 0.729 AC: 2534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533682; hg19: chr3-183634879;