chr10-117552592-C-T

Variant names:

• chr10-117552592-C-T
• rs4751627

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 0.518 in 152,106 control chromosomes in the GnomAD database, including 22,126 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 0.52 (22126 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78712 AN: 151988 Hom.: 22121 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.518 AC: 78742 AN: 152106 Hom.: 22126 Cov.: 33 AF XY: 0.514 AC XY: 38207 AN XY: 74390

African (AFR) AF: 0.293 AC: 12151 AN: 41492

American (AMR) AF: 0.574 AC: 8784 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1959 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2882 AN: 5152

South Asian (SAS) AF: 0.440 AC: 2119 AN: 4812

European-Finnish (FIN) AF: 0.561 AC: 5939 AN: 10594

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42905 AN: 67980

Other (OTH) AF: 0.585 AC: 1233 AN: 2108

Alfa AF: 0.422 Hom.: 1472

Bravo AF: 0.518

Asia WGS AF: 0.445 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4751627; hg19: chr10-119312103; COSMIC: COSV71294874;