rs41515647
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_030965.3(ST6GALNAC5):c.779+959C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,200 control chromosomes in the GnomAD database, including 168 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 0.044 ( 168 hom., cov: 32)
Consequence
ST6GALNAC5
NM_030965.3 intron
NM_030965.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0360
Genes affected
ST6GALNAC5 (HGNC:19342): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 5) The protein encoded by this gene is a Golgi type II transmembrane glycosyltransferase. The encoded protein catalyzes the transfer of sialic acid to cell surface proteins to modulate cell-cell interactions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0438 (6670/152200) while in subpopulation NFE AF= 0.0501 (3409/68012). AF 95% confidence interval is 0.0487. There are 168 homozygotes in gnomad4. There are 3162 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 168 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST6GALNAC5 | NM_030965.3 | c.779+959C>A | intron_variant | ENST00000477717.6 | |||
ST6GALNAC5 | NM_001320273.2 | c.*42+959C>A | intron_variant | ||||
ST6GALNAC5 | NM_001320274.2 | c.262-11651C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST6GALNAC5 | ENST00000477717.6 | c.779+959C>A | intron_variant | 1 | NM_030965.3 | P1 | |||
ST6GALNAC5 | ENST00000318803.6 | c.*64+959C>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0438 AC: 6668AN: 152082Hom.: 167 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0438 AC: 6670AN: 152200Hom.: 168 Cov.: 32 AF XY: 0.0425 AC XY: 3162AN XY: 74416
GnomAD4 genome
?
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32
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3162
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74416
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112
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at