11-41944809-C-T

Variant names:

• chr11-41944809-C-T
• rs10501281

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 0.0604 in 152,202 control chromosomes in the GnomAD database, including 335 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 0.060 (335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0761 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: 0.0605 AC: 9199 AN: 152084 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0604 AC: 9199 AN: 152202 Hom.: 335 Cov.: 32 AF XY: 0.0581 AC XY: 4323 AN XY: 74420

African (AFR) AF: 0.0449 AC: 1862 AN: 41506

American (AMR) AF: 0.0530 AC: 811 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3472

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5194

South Asian (SAS) AF: 0.0431 AC: 208 AN: 4826

European-Finnish (FIN) AF: 0.0503 AC: 533 AN: 10596

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0779 AC: 5297 AN: 67996

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0640 Hom.: 193

Bravo AF: 0.0603

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.79
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10501281; hg19: chr11-41966359;