12-4875435-C-T

Variant names:

• chr12-4875435-C-T
• rs2041377

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 0.203 in 152,104 control chromosomes in the GnomAD database, including 3,333 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 0.20 (3333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

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 = 0.29 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: 0.203 AC: 30791 AN: 151986 Hom.: 3326 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.203 AC: 30830 AN: 152104 Hom.: 3333 Cov.: 32 AF XY: 0.204 AC XY: 15173 AN XY: 74324

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.208

Alfa AF: 0.218 Hom.: 7776

Bravo AF: 0.190

Asia WGS AF: 0.268 AC: 932 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	5.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2041377; hg19: chr12-4984601;