rs187230

Positions:

• chr3-171552834-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.673

Alfa AF: 0.699 Hom.: 7550

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs187230; hg19: chr3-171270624;