ENST00000656102.1:n.552-1073C>T

Variant names:

• chr18-46766261-C-T
• rs17707448
• ENST00000656102.1:n.552-1073C>T

Variant summary

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

The ENST00000656102.1(ST8SIA5-DT):​n.552-1073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,102 control chromosomes in the GnomAD database, including 29,258 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 0.61 (29258 hom., cov: 33)
• Consequence: ST8SIA5-DT ENST00000656102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 6 publications found

Genes affected

ST8SIA5-DT (HGNC:55267): (ST8SIA5 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656102.1. 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
	ST8SIA5-DT	ENST00000656102.1		n.552-1073C>T		intron	N/A
	ST8SIA5-DT	ENST00000662459.1		n.549+5995C>T		intron	N/A
	ST8SIA5-DT	ENST00000663845.1		n.549+5995C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93314 AN: 151984 Hom.: 29215 Cov.: 33

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.614 AC: 93414 AN: 152102 Hom.: 29258 Cov.: 33 AF XY: 0.617 AC XY: 45856 AN XY: 74332

African (AFR) AF: 0.740 AC: 30704 AN: 41490

American (AMR) AF: 0.620 AC: 9475 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3596 AN: 5170

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6363 AN: 10568

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37230 AN: 67988

Other (OTH) AF: 0.601 AC: 1270 AN: 2112

Alfa AF: 0.592 Hom.: 12258

Bravo AF: 0.622

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs17707448; hg19: chr18-44346224;