chr10-12872521-C-A

Variant names:

• chr10-12872521-C-A
• rs4750277

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 0.774 in 152,030 control chromosomes in the GnomAD database, including 45,997 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 0.77 (45997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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: 0.774 AC: 117592 AN: 151912 Hom.: 45973 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.774 AC: 117667 AN: 152030 Hom.: 45997 Cov.: 31 AF XY: 0.773 AC XY: 57433 AN XY: 74324

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.778

Alfa AF: 0.825 Hom.: 109646

Bravo AF: 0.758

Asia WGS AF: 0.739 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750277; hg19: chr10-12914521;