10-118663672-C-T

Variant names:

• chr10-118663672-C-T
• rs873598

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 0.438 in 151,954 control chromosomes in the GnomAD database, including 14,819 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 0.44 (14819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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: 0.438 AC: 66544 AN: 151836 Hom.: 14801 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.438 AC: 66612 AN: 151954 Hom.: 14819 Cov.: 32 AF XY: 0.438 AC XY: 32547 AN XY: 74278

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.433

Alfa AF: 0.433 Hom.: 18729

Bravo AF: 0.447

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873598; hg19: chr10-120423184;