chr10-44361515-G-A

Variant names:

• chr10-44361515-G-A
• rs11239011

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 0.0581 in 152,312 control chromosomes in the GnomAD database, including 297 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 0.058 (297 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0911 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: 0.0580 AC: 8830 AN: 152194 Hom.: 296 Cov.: 33

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0581 AC: 8842 AN: 152312 Hom.: 297 Cov.: 33 AF XY: 0.0578 AC XY: 4306 AN XY: 74486

African (AFR) AF: 0.0349 AC: 1452 AN: 41562

American (AMR) AF: 0.0951 AC: 1456 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3470

East Asian (EAS) AF: 0.0432 AC: 224 AN: 5184

South Asian (SAS) AF: 0.0727 AC: 351 AN: 4830

European-Finnish (FIN) AF: 0.0472 AC: 501 AN: 10622

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0673 AC: 4577 AN: 68020

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0440 Hom.: 42

Bravo AF: 0.0605

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11239011; hg19: chr10-44856963;