16-55273177-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558730.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259283	ENST00000558730.2	TSL:3	n.216-6383G>A		intron	N/A

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

African (AFR) AF: 0.602 AC: 24923 AN: 41414

American (AMR) AF: 0.721 AC: 11006 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3777 AN: 5162

South Asian (SAS) AF: 0.646 AC: 3101 AN: 4800

European-Finnish (FIN) AF: 0.587 AC: 6190 AN: 10544

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43758 AN: 67962

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.644 Hom.: 59296

Bravo AF: 0.648

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.59
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs893265; hg19: chr16-55307089;