10-36823441-T-G

Position:

• chr10-36823441-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;