16-54503696-T-C

Position:

• chr16-54503696-T-C

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 0.137 in 152,186 control chromosomes in the GnomAD database, including 1,749 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 0.14 (1749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20760 AN: 152068 Hom.: 1748 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0308

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.137 AC: 20775 AN: 152186 Hom.: 1749 Cov.: 32 AF XY: 0.136 AC XY: 10111 AN XY: 74406

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0308

Gnomad4 EAS AF: 0.0257

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.122

Alfa AF: 0.105 Hom.: 1436

Bravo AF: 0.137

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.24
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8060871; hg19: chr16-54537608;