6-87477364-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006416.5(SLC35A1):āc.19A>Cā(p.Asn7His) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00107 in 1,612,270 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_006416.5 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC35A1 | NM_006416.5 | c.19A>C | p.Asn7His | missense_variant, splice_region_variant | Exon 2 of 8 | ENST00000369552.9 | NP_006407.1 | |
SLC35A1 | NM_001168398.2 | c.19A>C | p.Asn7His | missense_variant, splice_region_variant | Exon 2 of 7 | NP_001161870.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC35A1 | ENST00000369552.9 | c.19A>C | p.Asn7His | missense_variant, splice_region_variant | Exon 2 of 8 | 1 | NM_006416.5 | ENSP00000358565.4 | ||
ENSG00000213204 | ENST00000507897.5 | n.*63A>C | splice_region_variant, non_coding_transcript_exon_variant | Exon 14 of 16 | 2 | ENSP00000426769.1 | ||||
ENSG00000213204 | ENST00000507897.5 | n.*63A>C | 3_prime_UTR_variant | Exon 14 of 16 | 2 | ENSP00000426769.1 |
Frequencies
GnomAD3 genomes AF: 0.00570 AC: 868AN: 152172Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00144 AC: 360AN: 250156Hom.: 4 AF XY: 0.00103 AC XY: 140AN XY: 135306
GnomAD4 exome AF: 0.000586 AC: 855AN: 1459980Hom.: 7 Cov.: 31 AF XY: 0.000519 AC XY: 377AN XY: 726368
GnomAD4 genome AF: 0.00575 AC: 876AN: 152290Hom.: 2 Cov.: 32 AF XY: 0.00541 AC XY: 403AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
- -
- -
SLC35A1-congenital disorder of glycosylation Benign:1
- -
SLC35A1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at