10-124794280-C-T

Variant names:

• chr10-124794280-C-T
• rs11245366

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 0.483 in 152,022 control chromosomes in the GnomAD database, including 19,812 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 0.48 (19812 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 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: 0.483 AC: 73426 AN: 151904 Hom.: 19792 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.483 AC: 73464 AN: 152022 Hom.: 19812 Cov.: 33 AF XY: 0.491 AC XY: 36488 AN XY: 74300

African (AFR) AF: 0.223 AC: 9261 AN: 41460

American (AMR) AF: 0.590 AC: 9011 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2249 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3089 AN: 5170

South Asian (SAS) AF: 0.651 AC: 3139 AN: 4824

European-Finnish (FIN) AF: 0.603 AC: 6369 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38799 AN: 67966

Other (OTH) AF: 0.506 AC: 1066 AN: 2106

Alfa AF: 0.544 Hom.: 50538

Bravo AF: 0.467

Asia WGS AF: 0.594 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.79
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs11245366; hg19: chr10-126482849;