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rs289698

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152996.4(ST6GALNAC3):c.18+58527A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 152,254 control chromosomes in the GnomAD database, including 232 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 0.054 ( 232 hom., cov: 32)

Consequence

ST6GALNAC3
NM_152996.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.273
Variant links:
Genes affected
ST6GALNAC3 (HGNC:19343): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3) ST6GALNAC3 belongs to a family of sialyltransferases that transfer sialic acids from CMP-sialic acid to terminal positions of carbohydrate groups in glycoproteins and glycolipids (Lee et al., 1999 [PubMed 10207017]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ST6GALNAC3NM_152996.4 linkuse as main transcriptc.18+58527A>C intron_variant ENST00000328299.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ST6GALNAC3ENST00000328299.4 linkuse as main transcriptc.18+58527A>C intron_variant 1 NM_152996.4 P1Q8NDV1-1

Frequencies

GnomAD3 genomes
AF:
0.0537
AC:
8172
AN:
152136
Hom.:
232
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0558
Gnomad AMI
AF:
0.0978
Gnomad AMR
AF:
0.0302
Gnomad ASJ
AF:
0.0787
Gnomad EAS
AF:
0.0314
Gnomad SAS
AF:
0.0773
Gnomad FIN
AF:
0.0757
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.0529
Gnomad OTH
AF:
0.0421
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0537
AC:
8172
AN:
152254
Hom.:
232
Cov.:
32
AF XY:
0.0547
AC XY:
4077
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0557
Gnomad4 AMR
AF:
0.0302
Gnomad4 ASJ
AF:
0.0787
Gnomad4 EAS
AF:
0.0313
Gnomad4 SAS
AF:
0.0773
Gnomad4 FIN
AF:
0.0757
Gnomad4 NFE
AF:
0.0529
Gnomad4 OTH
AF:
0.0421
Alfa
AF:
0.0515
Hom.:
318
Bravo
AF:
0.0502
Asia WGS
AF:
0.0470
AC:
164
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
3.3
Dann
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs289698; hg19: chr1-76599096; API