5-15019551-A-G

Position:

• chr5-15019551-A-G

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 0.0854 in 152,248 control chromosomes in the GnomAD database, including 1,300 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 0.085 (1300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 12957 AN: 152130 Hom.: 1290 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00626

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0854 AC: 13004 AN: 152248 Hom.: 1300 Cov.: 32 AF XY: 0.0887 AC XY: 6605 AN XY: 74444

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0309

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0549

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.00628

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0171 Hom.: 321

Bravo AF: 0.0884

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513195; hg19: chr5-15019660;