16-56961078-C-T

Variant names:

• chr16-56961078-C-T
• rs17245715

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;