rs529515

Variant names:

• chr19-5445418-G-A
• rs529515

Your query was ambiguous. Multiple possible variants found:

• chr19-5445418-G-A
• chr19-5445418-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 0.652 in 151,374 control chromosomes in the GnomAD database, including 33,359 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 0.65 (33359 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98584 AN: 151262 Hom.: 33302 Cov.: 28

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.652 AC: 98696 AN: 151374 Hom.: 33359 Cov.: 28 AF XY: 0.657 AC XY: 48525 AN XY: 73900

African (AFR) AF: 0.824 AC: 34047 AN: 41300

American (AMR) AF: 0.609 AC: 9241 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4326 AN: 5124

South Asian (SAS) AF: 0.681 AC: 3272 AN: 4804

European-Finnish (FIN) AF: 0.608 AC: 6303 AN: 10368

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.552 AC: 37445 AN: 67830

Other (OTH) AF: 0.607 AC: 1273 AN: 2098

Alfa AF: 0.609 Hom.: 12392

Bravo AF: 0.662

Asia WGS AF: 0.799 AC: 2775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs529515; hg19: chr19-5445429; COSMIC: COSV50506438;