10-106441335-T-A

Variant names:

• chr10-106441335-T-A
• rs997422

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 0.651 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.785 AC: 32532 AN: 41418

American (AMR) AF: 0.575 AC: 8783 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2264 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4091 AN: 5138

South Asian (SAS) AF: 0.669 AC: 3220 AN: 4812

European-Finnish (FIN) AF: 0.527 AC: 5548 AN: 10536

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40307 AN: 67914

Other (OTH) AF: 0.669 AC: 1408 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.44
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs997422; hg19: chr10-108201093;