rs2731006

Variant names:

• chr12-42767023-C-T
• rs2731006

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 0.146 in 151,664 control chromosomes in the GnomAD database, including 2,140 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 0.15 (2140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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: 0.146 AC: 22195 AN: 151546 Hom.: 2134 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22206 AN: 151664 Hom.: 2140 Cov.: 32 AF XY: 0.153 AC XY: 11364 AN XY: 74114

Gnomad4 AFR AF: 0.0349

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.155

Alfa AF: 0.159 Hom.: 377

Bravo AF: 0.128

Asia WGS AF: 0.331 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2731006; hg19: chr12-43160825;