11-26748089-T-G

Variant names:

• chr11-26748089-T-G
• rs10501068

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 0.349 in 151,336 control chromosomes in the GnomAD database, including 11,582 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 0.35 (11582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.350 AC: 52872 AN: 151214 Hom.: 11584 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.00544

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.349 AC: 52863 AN: 151336 Hom.: 11582 Cov.: 32 AF XY: 0.350 AC XY: 25859 AN XY: 73922

African (AFR) AF: 0.124 AC: 5120 AN: 41422

American (AMR) AF: 0.311 AC: 4710 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1629 AN: 3448

East Asian (EAS) AF: 0.00545 AC: 28 AN: 5138

South Asian (SAS) AF: 0.281 AC: 1355 AN: 4814

European-Finnish (FIN) AF: 0.563 AC: 5945 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32717 AN: 67504

Other (OTH) AF: 0.390 AC: 820 AN: 2100

Alfa AF: 0.435 Hom.: 25495

Bravo AF: 0.320

Asia WGS AF: 0.143 AC: 499 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs10501068; hg19: chr11-26769636;