5-108706013-CTT-CT

Position:

• chr5-108706013-CTT-CT

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

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: 0.252 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

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.229

Bravo AF: 0.266

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;