10-12255231-C-T

Variant names:

• chr10-12255231-C-T
• rs4747969

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 0.803 in 151,730 control chromosomes in the GnomAD database, including 49,225 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 0.80 (49225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.849 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: 0.803 AC: 121736 AN: 151614 Hom.: 49185 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.803 AC: 121829 AN: 151730 Hom.: 49225 Cov.: 32 AF XY: 0.806 AC XY: 59752 AN XY: 74158

African (AFR) AF: 0.770 AC: 31649 AN: 41126

American (AMR) AF: 0.801 AC: 12218 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2788 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3428 AN: 5158

South Asian (SAS) AF: 0.871 AC: 4204 AN: 4826

European-Finnish (FIN) AF: 0.822 AC: 8699 AN: 10586

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56062 AN: 67994

Other (OTH) AF: 0.810 AC: 1705 AN: 2104

Alfa AF: 0.807 Hom.: 9424

Bravo AF: 0.797

Asia WGS AF: 0.774 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.20
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs4747969; hg19: chr10-12297230;