rs16949856

chr15-45980660-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 0.232 in 152,006 control chromosomes in the GnomAD database, including 4,354 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 (4354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.232 AC: 35301 AN: 151888 Hom.: 4348 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.00908

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.232 AC: 35317 AN: 152006 Hom.: 4354 Cov.: 32 AF XY: 0.230 AC XY: 17095 AN XY: 74300

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.00891

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.212

Alfa AF: 0.252 Hom.: 633

Bravo AF: 0.223

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949856; hg19: chr15-46272858;