10-106441335-T-A

Position:

• chr10-106441335-T-A

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 0.651 in 151,858 control chromosomes in the GnomAD database, including 32,899 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 0.65 (32899 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.106441335T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98719 AN: 151740 Hom.: 32863 Cov.: 30

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.651 AC: 98812 AN: 151858 Hom.: 32899 Cov.: 30 AF XY: 0.648 AC XY: 48047 AN XY: 74190

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.669

Alfa AF: 0.618 Hom.: 3703

Bravo AF: 0.658

Asia WGS AF: 0.710 AC: 2470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.44
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997422; hg19: chr10-108201093;