3-183917091-T-C

Variant names:

• chr3-183917091-T-C
• rs1533682

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.783 AC: 32495 AN: 41480

American (AMR) AF: 0.591 AC: 9030 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1963 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4329 AN: 5148

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5305 AN: 10590

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37869 AN: 67924

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.581 Hom.: 48038

Bravo AF: 0.642

Asia WGS AF: 0.729 AC: 2534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.4
DANN	Benign	0.49
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1533682; hg19: chr3-183634879;