rs4296809

Variant names:

• chr5-44186566-C-A
• rs4296809

Your query was ambiguous. Multiple possible variants found:

• chr5-44186566-C-A
• chr5-44186566-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.160 AC: 6622 AN: 41496

American (AMR) AF: 0.233 AC: 3543 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5150

South Asian (SAS) AF: 0.167 AC: 804 AN: 4820

European-Finnish (FIN) AF: 0.146 AC: 1539 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10894 AN: 67948

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.162 Hom.: 7426

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4296809; hg19: chr5-44186668;