chr10-12265895-C-T

Variant names:

• chr10-12265895-C-T
• rs11257655

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 0.238 in 151,924 control chromosomes in the GnomAD database, including 4,656 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 0.24 (4656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 165 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 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: 0.238 AC: 36063 AN: 151806 Hom.: 4655 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.238 AC: 36093 AN: 151924 Hom.: 4656 Cov.: 31 AF XY: 0.241 AC XY: 17887 AN XY: 74240

African (AFR) AF: 0.257 AC: 10633 AN: 41410

American (AMR) AF: 0.223 AC: 3398 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2743 AN: 5158

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4822

European-Finnish (FIN) AF: 0.278 AC: 2935 AN: 10548

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13676 AN: 67956

Other (OTH) AF: 0.226 AC: 476 AN: 2110

Alfa AF: 0.216 Hom.: 16200

Bravo AF: 0.239

Asia WGS AF: 0.356 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.65
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs11257655; hg19: chr10-12307894;