rs983154

Variant names:

• chr3-3666318-C-T
• rs983154

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 0.512 in 152,022 control chromosomes in the GnomAD database, including 20,396 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 0.51 (20396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.512 AC: 77774 AN: 151902 Hom.: 20361 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.512 AC: 77865 AN: 152022 Hom.: 20396 Cov.: 32 AF XY: 0.514 AC XY: 38203 AN XY: 74310

African (AFR) AF: 0.582 AC: 24136 AN: 41452

American (AMR) AF: 0.558 AC: 8520 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1959 AN: 3472

East Asian (EAS) AF: 0.723 AC: 3722 AN: 5146

South Asian (SAS) AF: 0.533 AC: 2572 AN: 4826

European-Finnish (FIN) AF: 0.426 AC: 4499 AN: 10556

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30919 AN: 67974

Other (OTH) AF: 0.509 AC: 1077 AN: 2114

Alfa AF: 0.480 Hom.: 75567

Bravo AF: 0.525

Asia WGS AF: 0.612 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs983154; hg19: chr3-3708002;