chr3-98723857-C-T

Variant names:

• chr3-98723857-C-T
• rs7628381
• ENST00000461931.1:n.227-5336G>A

Variant summary

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

The ENST00000461931.1(ST3GAL6-AS1):​n.227-5336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,968 control chromosomes in the GnomAD database, including 8,454 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 0.32 (8454 hom., cov: 32)
• Consequence: ST3GAL6-AS1 ENST00000461931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL6-AS1	NR_046683.1	n.227-5336G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL6-AS1	ENST00000461931.1	n.227-5336G>A		intron_variant	Intron 1 of 3	2
ST3GAL6-AS1	ENST00000475816.6	n.197-8080G>A		intron_variant	Intron 1 of 3	3
ST3GAL6-AS1	ENST00000488132.6	n.83-5336G>A		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49182 AN: 151846 Hom.: 8443 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.324 AC: 49223 AN: 151968 Hom.: 8454 Cov.: 32 AF XY: 0.327 AC XY: 24287 AN XY: 74262

African (AFR) AF: 0.380 AC: 15733 AN: 41422

American (AMR) AF: 0.417 AC: 6378 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1970 AN: 5158

South Asian (SAS) AF: 0.412 AC: 1987 AN: 4820

European-Finnish (FIN) AF: 0.291 AC: 3064 AN: 10542

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18427 AN: 67958

Other (OTH) AF: 0.318 AC: 669 AN: 2106

Alfa AF: 0.278 Hom.: 9374

Bravo AF: 0.333

Asia WGS AF: 0.330 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7628381; hg19: chr3-98442701;