chr5-109927521-CT-C

Position:

• chr5-109927521-CT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.0636 in 152,184 control chromosomes in the GnomAD database, including 811 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9644 AN: 152068 Hom.: 806 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0636 AC: 9677 AN: 152184 Hom.: 811 Cov.: 32 AF XY: 0.0621 AC XY: 4619 AN XY: 74404

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.00336 Hom.: 1

Bravo AF: 0.0708

Asia WGS AF: 0.0660 AC: 229 AN: 3478

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: rs11301693; hg19: chr5-109263222;