16-55273177-C-T

Variant names:

• chr16-55273177-C-T
• rs893265
• ENST00000558730.2:n.216-6383G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558730.2(ENSG00000259283):​n.216-6383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,938 control chromosomes in the GnomAD database, including 30,858 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 0.64 (30858 hom., cov: 31)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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
ENSG00000259283	ENST00000558730.2	n.216-6383G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96666 AN: 151820 Hom.: 30825 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.637 AC: 96756 AN: 151938 Hom.: 30858 Cov.: 31 AF XY: 0.638 AC XY: 47355 AN XY: 74238

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.631

Alfa AF: 0.642 Hom.: 42583

Bravo AF: 0.648

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs893265; hg19: chr16-55307089;