5-108706013-CTT-CT

Variant names:

• chr5-108706013-CT-C
• rs10707846

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.252 in 147,640 control chromosomes in the GnomAD database, including 6,510 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (6510 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 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: 0.252 AC: 37193 AN: 147568 Hom.: 6500 Cov.: 22

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.252 AC: 37237 AN: 147640 Hom.: 6510 Cov.: 22 AF XY: 0.246 AC XY: 17698 AN XY: 71870

African (AFR) AF: 0.507 AC: 20543 AN: 40506

American (AMR) AF: 0.154 AC: 2280 AN: 14776

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 558 AN: 3414

East Asian (EAS) AF: 0.0650 AC: 329 AN: 5064

South Asian (SAS) AF: 0.103 AC: 479 AN: 4636

European-Finnish (FIN) AF: 0.153 AC: 1453 AN: 9482

Middle Eastern (MID) AF: 0.218 AC: 62 AN: 284

European-Non Finnish (NFE) AF: 0.163 AC: 10829 AN: 66552

Other (OTH) AF: 0.229 AC: 466 AN: 2036

Alfa AF: 0.0691 Hom.: 75

Bravo AF: 0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10707846; hg19: chr5-108041714;