rs17550532

Variant names:

• chr16-9650238-A-G
• rs17550532

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 0.17 in 152,170 control chromosomes in the GnomAD database, including 2,433 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 0.17 (2433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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: 0.171 AC: 25929 AN: 152052 Hom.: 2435 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.170 AC: 25934 AN: 152170 Hom.: 2433 Cov.: 32 AF XY: 0.167 AC XY: 12390 AN XY: 74406

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.204

Alfa AF: 0.203 Hom.: 6839

Bravo AF: 0.167

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17550532; hg19: chr16-9744095;