10-36823441-T-G

Variant names:

• chr10-36823441-T-G
• rs2490841

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 0.129 in 152,158 control chromosomes in the GnomAD database, including 1,588 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 0.13 (1588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.128 AC: 19533 AN: 152040 Hom.: 1574 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0822

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.129 AC: 19594 AN: 152158 Hom.: 1588 Cov.: 32 AF XY: 0.125 AC XY: 9302 AN XY: 74392

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.0822

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.0957

Gnomad4 OTH AF: 0.109

Alfa AF: 0.115 Hom.: 152

Bravo AF: 0.131

Asia WGS AF: 0.0700 AC: 243 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	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2490841; hg19: chr10-37112369;