chr5-15039218-G-A

Variant names:

• chr5-15039218-G-A
• rs735243

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 0.197 in 151,864 control chromosomes in the GnomAD database, including 3,297 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 0.20 (3297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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: 0.197 AC: 29906 AN: 151746 Hom.: 3294 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.197 AC: 29941 AN: 151864 Hom.: 3297 Cov.: 32 AF XY: 0.197 AC XY: 14595 AN XY: 74210

African (AFR) AF: 0.289 AC: 11943 AN: 41386

American (AMR) AF: 0.160 AC: 2440 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1268 AN: 5170

South Asian (SAS) AF: 0.125 AC: 600 AN: 4812

European-Finnish (FIN) AF: 0.198 AC: 2082 AN: 10534

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10182 AN: 67920

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.165 Hom.: 4027

Bravo AF: 0.201

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs735243; hg19: chr5-15039327;