rs597804

Variant names:

• chr15-57808751-G-A
• rs597804

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 0.712 in 152,112 control chromosomes in the GnomAD database, including 38,850 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 0.71 (38850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 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: 0.713 AC: 108314 AN: 151994 Hom.: 38845 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.712 AC: 108359 AN: 152112 Hom.: 38850 Cov.: 32 AF XY: 0.712 AC XY: 52903 AN XY: 74342

African (AFR) AF: 0.651 AC: 26989 AN: 41482

American (AMR) AF: 0.677 AC: 10354 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2392 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2891 AN: 5164

South Asian (SAS) AF: 0.666 AC: 3204 AN: 4812

European-Finnish (FIN) AF: 0.778 AC: 8240 AN: 10586

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52051 AN: 67992

Other (OTH) AF: 0.719 AC: 1519 AN: 2114

Alfa AF: 0.738 Hom.: 142714

Bravo AF: 0.698

Asia WGS AF: 0.631 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.012
DANN	Benign	0.66
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs597804; hg19: chr15-58100949;