rs732505

Variant names:

• chr19-5582524-G-A
• rs732505

Your query was ambiguous. Multiple possible variants found:

• chr19-5582524-G-A
• chr19-5582524-G-C

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 0.103 in 152,206 control chromosomes in the GnomAD database, including 1,076 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 0.10 (1076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 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: 0.103 AC: 15696 AN: 152088 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.103 AC: 15746 AN: 152206 Hom.: 1076 Cov.: 32 AF XY: 0.104 AC XY: 7714 AN XY: 74418

African (AFR) AF: 0.192 AC: 7989 AN: 41502

American (AMR) AF: 0.0680 AC: 1039 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3472

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5184

South Asian (SAS) AF: 0.109 AC: 525 AN: 4814

European-Finnish (FIN) AF: 0.0737 AC: 783 AN: 10620

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0672 AC: 4569 AN: 68006

Other (OTH) AF: 0.0969 AC: 205 AN: 2116

Alfa AF: 0.0761 Hom.: 2042

Bravo AF: 0.105

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.56
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs732505; hg19: chr19-5582535;