10-111282335-T-G

Variant names:

• chr10-111282335-T-G
• rs10885122

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 0.715 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.716 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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.757

Alfa AF: 0.857 Hom.: 105696

Bravo AF: 0.697

Asia WGS AF: 0.804 AC: 2797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885122; hg19: chr10-113042093;