16-55713265-C-T

Variant names:

• chr16-55713265-C-T
• rs258099

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 0.555 in 151,654 control chromosomes in the GnomAD database, including 26,512 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 0.56 (26512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 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: 0.555 AC: 84163 AN: 151534 Hom.: 26494 Cov.: 30

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.555 AC: 84196 AN: 151654 Hom.: 26512 Cov.: 30 AF XY: 0.551 AC XY: 40821 AN XY: 74048

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.569

Alfa AF: 0.657 Hom.: 11877

Bravo AF: 0.545

Asia WGS AF: 0.437 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258099; hg19: chr16-55747177;