10-111282335-T-G

Variant names:

• chr10-111282335-T-G
• rs10885122

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 0.715 in 152,040 control chromosomes in the GnomAD database, including 43,396 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 0.72 (43396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 103 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108744 AN: 151922 Hom.: 43393 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.715 AC: 108759 AN: 152040 Hom.: 43396 Cov.: 31 AF XY: 0.719 AC XY: 53463 AN XY: 74316

African (AFR) AF: 0.321 AC: 13311 AN: 41438

American (AMR) AF: 0.829 AC: 12675 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3062 AN: 3470

East Asian (EAS) AF: 0.932 AC: 4801 AN: 5154

South Asian (SAS) AF: 0.794 AC: 3821 AN: 4814

European-Finnish (FIN) AF: 0.852 AC: 9005 AN: 10564

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59499 AN: 67996

Other (OTH) AF: 0.757 AC: 1601 AN: 2114

Alfa AF: 0.832 Hom.: 232419

Bravo AF: 0.697

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10885122; hg19: chr10-113042093;