chr10-118663672-C-T

Variant names:

• chr10-118663672-C-T
• rs873598

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.407 AC: 16853 AN: 41446

American (AMR) AF: 0.507 AC: 7750 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3134 AN: 5156

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4818

European-Finnish (FIN) AF: 0.397 AC: 4181 AN: 10538

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29793 AN: 67924

Other (OTH) AF: 0.433 AC: 914 AN: 2110

Alfa AF: 0.435 Hom.: 23086

Bravo AF: 0.447

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.32
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs873598; hg19: chr10-120423184;