rs17245715

Positions:

• chr16-56961078-C-T

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 0.106 in 458,552 control chromosomes in the GnomAD database, including 3,157 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 0.090 (843 hom., cov: 33)
  • Exomes 𝑓: 0.11 (2314 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13629 AN: 152182 Hom.: 841 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.115 AC: 35166 AN: 306252 Hom.: 2314 AF XY: 0.118 AC XY: 20557 AN XY: 174464

Gnomad4 AFR exome AF: 0.0196

Gnomad4 AMR exome AF: 0.145

Gnomad4 ASJ exome AF: 0.112

Gnomad4 EAS exome AF: 0.223

Gnomad4 SAS exome AF: 0.147

Gnomad4 FIN exome AF: 0.150

Gnomad4 NFE exome AF: 0.0940

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.0896 AC: 13639 AN: 152300 Hom.: 843 Cov.: 33 AF XY: 0.0958 AC XY: 7133 AN XY: 74464

Gnomad4 AFR AF: 0.0206

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.0968

Gnomad4 OTH AF: 0.105

Alfa AF: 0.100 Hom.: 175

Bravo AF: 0.0853

Asia WGS AF: 0.189 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.5
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17245715; hg19: chr16-56994990; COSMIC: COSV52364059;