rs512692

Variant names:

• chr3-172453052-A-T
• rs512692

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 0.228 in 151,922 control chromosomes in the GnomAD database, including 4,639 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 0.23 (4639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.228 AC: 34631 AN: 151804 Hom.: 4632 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.228 AC: 34661 AN: 151922 Hom.: 4639 Cov.: 32 AF XY: 0.231 AC XY: 17114 AN XY: 74234

Gnomad4 AFR AF: 0.0931

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.216

Alfa AF: 0.245 Hom.: 605

Bravo AF: 0.227

Asia WGS AF: 0.269 AC: 935 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs512692; hg19: chr3-172170842;