rs2737447

Variant names:

• chr12-28000594-T-C
• rs2737447

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 0.0853 in 152,196 control chromosomes in the GnomAD database, including 702 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 0.085 (702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.0854 AC: 12980 AN: 152078 Hom.: 702 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0853 AC: 12980 AN: 152196 Hom.: 702 Cov.: 32 AF XY: 0.0832 AC XY: 6189 AN XY: 74420

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0761

Alfa AF: 0.105 Hom.: 231

Bravo AF: 0.0840

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2737447; hg19: chr12-28153527;