10-111282335-T-G

Position:

• chr10-111282335-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 0.715 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/exons	MANE	UniProt

Ensembl

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