rs12631899

Positions:

• chr3-144550013-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;