5-108706013-CTT-CTTT

Variant names:

• chr5-108706013-C-CT
• rs10707846

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The variant allele was found at a frequency of 0.00926 in 147,796 control chromosomes in the GnomAD database, including 8 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0093 (8 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00926 (1368/147796) while in subpopulation AFR AF = 0.0204 (828/40536). AF 95% confidence interval is 0.0193. There are 8 homozygotes in GnomAd4. There are 653 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 8 gene

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: 0.00921 AC: 1360 AN: 147724 Hom.: 8 Cov.: 22

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.00113

Gnomad AMR AF: 0.00751

Gnomad ASJ AF: 0.000879

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00108

Gnomad FIN AF: 0.00588

Gnomad MID AF: 0.00974

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.00742

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

GnomAD4 genome AF: 0.00926 AC: 1368 AN: 147796 Hom.: 8 Cov.: 22 AF XY: 0.00908 AC XY: 653 AN XY: 71948

African (AFR) AF: 0.0204 AC: 828 AN: 40536

American (AMR) AF: 0.00751 AC: 111 AN: 14790

Ashkenazi Jewish (ASJ) AF: 0.000879 AC: 3 AN: 3414

East Asian (EAS) AF: 0.000197 AC: 1 AN: 5066

South Asian (SAS) AF: 0.00108 AC: 5 AN: 4636

European-Finnish (FIN) AF: 0.00588 AC: 56 AN: 9524

Middle Eastern (MID) AF: 0.0141 AC: 4 AN: 284

European-Non Finnish (NFE) AF: 0.00516 AC: 344 AN: 66618

Other (OTH) AF: 0.00735 AC: 15 AN: 2040

Alfa AF: 0.000811 Hom.: 75

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10707846;

hg19: chr5-108041714;