rs12631899

Variant names:

• chr3-144550013-T-C
• rs12631899

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 0.16 in 152,162 control chromosomes in the GnomAD database, including 2,637 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 0.16 (2637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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: 0.160 AC: 24292 AN: 152044 Hom.: 2627 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.160 AC: 24323 AN: 152162 Hom.: 2637 Cov.: 32 AF XY: 0.160 AC XY: 11924 AN XY: 74396

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.150

Alfa AF: 0.104 Hom.: 1005

Bravo AF: 0.169

Asia WGS AF: 0.266 AC: 924 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.86
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12631899; hg19: chr3-144268855;