rs17707448

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA5-DT	XR_001753432.3	n.2487+5995C>T		intron_variant	Intron 2 of 3
ST8SIA5-DT	XR_001753433.3	n.2488-1073C>T		intron_variant	Intron 2 of 4
ST8SIA5-DT	XR_001753434.3	n.2487+5995C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA5-DT	ENST00000656102.1	n.552-1073C>T		intron_variant	Intron 2 of 2
ST8SIA5-DT	ENST00000662459.1	n.549+5995C>T		intron_variant	Intron 2 of 3
ST8SIA5-DT	ENST00000663845.1	n.549+5995C>T		intron_variant	Intron 2 of 3

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 v4.3

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;