5-108706013-CTT-CTTT

Position:

• chr5-108706013-CTT-CTTT

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.00751

Gnomad4 ASJ AF: 0.000879

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00108

Gnomad4 FIN AF: 0.00588

Gnomad4 NFE AF: 0.00516

Gnomad4 OTH AF: 0.00735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10707846; hg19: chr5-108041714;