10-111155014-C-T

Variant names:

• chr10-111155014-C-T
• rs1335706

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 0.507 in 151,986 control chromosomes in the GnomAD database, including 21,334 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 0.51 (21334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.507 AC: 76964 AN: 151868 Hom.: 21283 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.507 AC: 77070 AN: 151986 Hom.: 21334 Cov.: 32 AF XY: 0.509 AC XY: 37835 AN XY: 74288

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.506

Alfa AF: 0.424 Hom.: 3485

Bravo AF: 0.531

Asia WGS AF: 0.622 AC: 2158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335706; hg19: chr10-112914772;