5-15019551-A-G

Variant names:

• chr5-15019551-A-G
• rs10513195

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;