rs4296809

chr5-44186566-C-Achr5-44186566-C-T

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 0.168 in 151,996 control chromosomes in the GnomAD database, including 2,213 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 0.17 (2213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 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: 0.168 AC: 25443 AN: 151880 Hom.: 2199 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.168 AC: 25500 AN: 151996 Hom.: 2213 Cov.: 32 AF XY: 0.168 AC XY: 12478 AN XY: 74260

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.178

Alfa AF: 0.158 Hom.: 3266

Bravo AF: 0.172

Asia WGS AF: 0.216 AC: 750 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.15
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4296809; hg19: chr5-44186668;