5-15019551-A-G

Variant names:

• chr5-15019551-A-G
• rs10513195

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 0.0854 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.228 AC: 9451 AN: 41506

American (AMR) AF: 0.0309 AC: 473 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1296 AN: 5192

South Asian (SAS) AF: 0.0549 AC: 265 AN: 4830

European-Finnish (FIN) AF: 0.0823 AC: 872 AN: 10598

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00628 AC: 427 AN: 68026

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0295 Hom.: 1625

Bravo AF: 0.0884

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10513195; hg19: chr5-15019660;