5-15364375-G-A

Position:

• chr5-15364375-G-A

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 0.204 in 152,148 control chromosomes in the GnomAD database, including 3,549 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 (3549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.204 AC: 31069 AN: 152030 Hom.: 3543 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.204 AC: 31087 AN: 152148 Hom.: 3549 Cov.: 32 AF XY: 0.203 AC XY: 15067 AN XY: 74366

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.232

Alfa AF: 0.226 Hom.: 8418

Bravo AF: 0.198

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1447276; hg19: chr5-15364484;