5-15001820-C-T

Variant names:

• chr5-15001820-C-T
• rs9312876

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.184 in 152,096 control chromosomes in the GnomAD database, including 2,657 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 0.18 (2657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 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: 0.184 AC: 28025 AN: 151978 Hom.: 2656 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.184 AC: 28044 AN: 152096 Hom.: 2657 Cov.: 32 AF XY: 0.184 AC XY: 13658 AN XY: 74324

African (AFR) AF: 0.194 AC: 8039 AN: 41486

American (AMR) AF: 0.159 AC: 2435 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5156

South Asian (SAS) AF: 0.169 AC: 815 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10572

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12046 AN: 67996

Other (OTH) AF: 0.210 AC: 443 AN: 2108

Alfa AF: 0.180 Hom.: 9597

Bravo AF: 0.183

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs9312876; hg19: chr5-15001929;