3-98726480-A-G

Variant names:

• chr3-98726480-A-G
• rs865474
• ENST00000461931.1:n.226+5946T>C

Variant summary

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

The ENST00000461931.1(ST3GAL6-AS1):​n.226+5946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,112 control chromosomes in the GnomAD database, including 22,077 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 0.53 (22077 hom., cov: 33)
• Consequence: ST3GAL6-AS1 ENST00000461931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 6 publications found

Genes affected

ST3GAL6-AS1 (HGNC:40828): (ST3GAL6 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL6-AS1	NR_046683.1	n.226+5946T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL6-AS1	ENST00000461931.1	n.226+5946T>C		intron_variant	Intron 1 of 3	2
ST3GAL6-AS1	ENST00000475816.6	n.196+5946T>C		intron_variant	Intron 1 of 3	3
ST3GAL6-AS1	ENST00000488132.6	n.82+5946T>C		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80296 AN: 151994 Hom.: 22037 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 80395 AN: 152112 Hom.: 22077 Cov.: 33 AF XY: 0.527 AC XY: 39228 AN XY: 74374

African (AFR) AF: 0.670 AC: 27819 AN: 41500

American (AMR) AF: 0.583 AC: 8917 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2363 AN: 5176

South Asian (SAS) AF: 0.561 AC: 2708 AN: 4824

European-Finnish (FIN) AF: 0.419 AC: 4427 AN: 10572

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31021 AN: 67970

Other (OTH) AF: 0.524 AC: 1105 AN: 2108

Alfa AF: 0.478 Hom.: 25502

Bravo AF: 0.544

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs865474; hg19: chr3-98445324;