chr5-109989667-A-G

Position:

• chr5-109989667-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0259 in 152,244 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.026 (106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0645 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: 0.0258 AC: 3918 AN: 152126 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00750

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0259 AC: 3938 AN: 152244 Hom.: 106 Cov.: 32 AF XY: 0.0255 AC XY: 1899 AN XY: 74444

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0123

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00750

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0189 Hom.: 14

Bravo AF: 0.0283

Asia WGS AF: 0.0580 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735350; hg19: chr5-109325368;