12-38590883-C-T

Variant names:

• chr12-38590883-C-T
• rs2730891

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.708 AC: 29352 AN: 41472

American (AMR) AF: 0.214 AC: 3267 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0892 AC: 309 AN: 3464

East Asian (EAS) AF: 0.460 AC: 2373 AN: 5160

South Asian (SAS) AF: 0.203 AC: 979 AN: 4822

European-Finnish (FIN) AF: 0.0443 AC: 469 AN: 10580

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3847 AN: 67994

Other (OTH) AF: 0.224 AC: 472 AN: 2104

Alfa AF: 0.197 Hom.: 1020

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2730891; hg19: chr12-38984685;