11-123756028-C-T

Variant names:

• chr11-123756028-C-T
• rs10502268

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 0.514 in 149,930 control chromosomes in the GnomAD database, including 20,229 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 0.51 (20229 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.514 AC: 77047 AN: 149822 Hom.: 20234 Cov.: 30

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.711

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.514 AC: 77057 AN: 149930 Hom.: 20229 Cov.: 30 AF XY: 0.508 AC XY: 37140 AN XY: 73060

African (AFR) AF: 0.480 AC: 19495 AN: 40578

American (AMR) AF: 0.449 AC: 6765 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2056 AN: 3428

East Asian (EAS) AF: 0.206 AC: 1043 AN: 5054

South Asian (SAS) AF: 0.425 AC: 2017 AN: 4748

European-Finnish (FIN) AF: 0.541 AC: 5529 AN: 10214

Middle Eastern (MID) AF: 0.724 AC: 207 AN: 286

European-Non Finnish (NFE) AF: 0.569 AC: 38418 AN: 67572

Other (OTH) AF: 0.538 AC: 1119 AN: 2080

Alfa AF: 0.549 Hom.: 69854

Bravo AF: 0.502

Asia WGS AF: 0.303 AC: 1049 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10502268; hg19: chr11-123626736;