chr16-54483570-C-T

Variant names:

• chr16-54483570-C-T
• rs733017

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.495 in 152,006 control chromosomes in the GnomAD database, including 19,980 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 0.50 (19980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 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: 0.496 AC: 75267 AN: 151888 Hom.: 19979 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.495 AC: 75295 AN: 152006 Hom.: 19980 Cov.: 33 AF XY: 0.492 AC XY: 36580 AN XY: 74294

African (AFR) AF: 0.337 AC: 13952 AN: 41458

American (AMR) AF: 0.496 AC: 7582 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1187 AN: 5158

South Asian (SAS) AF: 0.360 AC: 1734 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6562 AN: 10556

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41076 AN: 67970

Other (OTH) AF: 0.509 AC: 1070 AN: 2104

Alfa AF: 0.559 Hom.: 92485

Bravo AF: 0.481

Asia WGS AF: 0.277 AC: 965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs733017; hg19: chr16-54517482;