rs597804

Variant names:

• chr15-57808751-G-A
• rs597804

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 0.712 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.713 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

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.719

Alfa AF: 0.747 Hom.: 89889

Bravo AF: 0.698

Asia WGS AF: 0.631 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs597804; hg19: chr15-58100949;