10-42844682-T-C

Variant names:

• chr10-42844682-T-C
• rs2744088

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.866 in 151,956 control chromosomes in the GnomAD database, including 57,087 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 0.87 (57087 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.866 AC: 131423 AN: 151838 Hom.: 57035 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.866 AC: 131534 AN: 151956 Hom.: 57087 Cov.: 30 AF XY: 0.866 AC XY: 64311 AN XY: 74272

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.835

Gnomad4 OTH AF: 0.866

Alfa AF: 0.852 Hom.: 9342

Bravo AF: 0.867

Asia WGS AF: 0.820 AC: 2853 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2744088; hg19: chr10-43340130;