chr10-110165059-C-T

Variant names:

• chr10-110165059-C-T
• rs12243027

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 0.361 in 151,844 control chromosomes in the GnomAD database, including 15,565 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 0.36 (15565 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.361 AC: 54769 AN: 151726 Hom.: 15512 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.361 AC: 54882 AN: 151844 Hom.: 15565 Cov.: 31 AF XY: 0.361 AC XY: 26769 AN XY: 74194

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.328

Alfa AF: 0.262 Hom.: 2780

Bravo AF: 0.381

Asia WGS AF: 0.510 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.017
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12243027; hg19: chr10-111924817;