chr3-98723857-C-T

Position:

• chr3-98723857-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046683.1(ST3GAL6-AS1):​n.227-5336G>A variant causes a intron, non coding transcript 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 NR_046683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ST3GAL6-AS1	NR_046683.1	n.227-5336G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL6-AS1	ENST00000670291.1	n.333-5336G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.318

Alfa AF: 0.276 Hom.: 7794

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628381; hg19: chr3-98442701;