10-117555813-C-T

Variant names:

• chr10-117555813-C-T
• rs8181280

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 0.519 in 152,066 control chromosomes in the GnomAD database, including 22,199 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 (22199 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• 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 = 0.627 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: 0.519 AC: 78899 AN: 151948 Hom.: 22194 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.519 AC: 78931 AN: 152066 Hom.: 22199 Cov.: 33 AF XY: 0.515 AC XY: 38274 AN XY: 74366

African (AFR) AF: 0.296 AC: 12279 AN: 41482

American (AMR) AF: 0.575 AC: 8790 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1955 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2881 AN: 5148

South Asian (SAS) AF: 0.440 AC: 2122 AN: 4828

European-Finnish (FIN) AF: 0.560 AC: 5932 AN: 10584

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42969 AN: 67956

Other (OTH) AF: 0.585 AC: 1232 AN: 2106

Alfa AF: 0.600 Hom.: 116903

Bravo AF: 0.519

Asia WGS AF: 0.441 AC: 1537 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	3.0
DANN	Benign	0.46
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs8181280; hg19: chr10-119315324;