3-183917980-C-T

Variant names:

• chr3-183917980-C-T
• rs1000002

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 0.388 in 152,118 control chromosomes in the GnomAD database, including 12,812 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 0.39 (12812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59000 AN: 152000 Hom.: 12805 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.388 AC: 59028 AN: 152118 Hom.: 12812 Cov.: 32 AF XY: 0.386 AC XY: 28713 AN XY: 74340

African (AFR) AF: 0.182 AC: 7550 AN: 41530

American (AMR) AF: 0.436 AC: 6660 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2592 AN: 5172

South Asian (SAS) AF: 0.435 AC: 2087 AN: 4800

European-Finnish (FIN) AF: 0.400 AC: 4224 AN: 10566

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32923 AN: 67990

Other (OTH) AF: 0.441 AC: 932 AN: 2112

Alfa AF: 0.447 Hom.: 42570

Bravo AF: 0.382

Asia WGS AF: 0.470 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.4
DANN	Benign	0.65
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1000002; hg19: chr3-183635768;