rs17776563

Variant names:

• chr15-88575873-G-A
• rs17776563

Your query was ambiguous. Multiple possible variants found:

• chr15-88575873-G-A
• chr15-88575873-G-C

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 0.227 in 152,126 control chromosomes in the GnomAD database, including 4,895 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 0.23 (4895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.227 AC: 34493 AN: 152008 Hom.: 4900 Cov.: 32

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.227 AC: 34483 AN: 152126 Hom.: 4895 Cov.: 32 AF XY: 0.225 AC XY: 16700 AN XY: 74344

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.267

Alfa AF: 0.151 Hom.: 330

Bravo AF: 0.214

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17776563; hg19: chr15-89119104;