12-38590883-C-T

Variant names:

• chr12-38590883-C-T
• rs2730891

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 0.271 in 152,074 control chromosomes in the GnomAD database, including 11,803 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 0.27 (11803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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: 0.271 AC: 41113 AN: 151954 Hom.: 11750 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0892

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.271 AC: 41235 AN: 152074 Hom.: 11803 Cov.: 32 AF XY: 0.270 AC XY: 20087 AN XY: 74342

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.0892

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.224

Alfa AF: 0.178 Hom.: 849

Bravo AF: 0.304

Asia WGS AF: 0.352 AC: 1225 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2730891; hg19: chr12-38984685;