rs1881984

Variant names:

• chr3-169746671-A-G
• rs1881984

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 0.307 in 151,724 control chromosomes in the GnomAD database, including 7,423 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 0.31 (7423 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.307 AC: 46506 AN: 151606 Hom.: 7411 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.307 AC: 46560 AN: 151724 Hom.: 7423 Cov.: 31 AF XY: 0.308 AC XY: 22856 AN XY: 74124

African (AFR) AF: 0.237 AC: 9782 AN: 41326

American (AMR) AF: 0.297 AC: 4527 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1989 AN: 5148

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3638 AN: 10474

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22806 AN: 67932

Other (OTH) AF: 0.295 AC: 621 AN: 2106

Alfa AF: 0.331 Hom.: 8780

Bravo AF: 0.298

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1881984; hg19: chr3-169464459;