rs173539

Variant names:

• chr16-56954132-C-T
• rs173539

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 0.333 in 151,824 control chromosomes in the GnomAD database, including 8,623 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 0.33 (8623 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 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: 0.333 AC: 50542 AN: 151708 Hom.: 8608 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.333 AC: 50592 AN: 151824 Hom.: 8623 Cov.: 31 AF XY: 0.331 AC XY: 24579 AN XY: 74184

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.300

Alfa AF: 0.330 Hom.: 10355

Bravo AF: 0.335

Asia WGS AF: 0.278 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs173539; hg19: chr16-56988044;