rs187230

Variant names:

• chr3-171552834-C-A
• rs187230

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 0.686 in 151,986 control chromosomes in the GnomAD database, including 36,169 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 0.69 (36169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 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: 0.686 AC: 104254 AN: 151868 Hom.: 36149 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.686 AC: 104319 AN: 151986 Hom.: 36169 Cov.: 31 AF XY: 0.683 AC XY: 50745 AN XY: 74316

African (AFR) AF: 0.703 AC: 29124 AN: 41402

American (AMR) AF: 0.637 AC: 9727 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1843 AN: 5164

South Asian (SAS) AF: 0.610 AC: 2933 AN: 4812

European-Finnish (FIN) AF: 0.754 AC: 7971 AN: 10568

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 48003 AN: 67984

Other (OTH) AF: 0.673 AC: 1422 AN: 2112

Alfa AF: 0.700 Hom.: 7752

Bravo AF: 0.673

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.50
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs187230; hg19: chr3-171270624;