NM_001011551.3:c.302G>A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001011551.3(C1GALT1C1):c.302G>A(p.Ser101Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00739 in 1,209,810 control chromosomes in the GnomAD database, including 31 homozygotes. There are 2,754 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001011551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1GALT1C1 | ENST00000304661.6 | c.302G>A | p.Ser101Asn | missense_variant | Exon 2 of 2 | 1 | NM_001011551.3 | ENSP00000304364.5 | ||
C1GALT1C1 | ENST00000371313.2 | c.302G>A | p.Ser101Asn | missense_variant | Exon 3 of 3 | 1 | ENSP00000360363.2 |
Frequencies
GnomAD3 genomes AF: 0.00478 AC: 535AN: 111834Hom.: 2 Cov.: 23 AF XY: 0.00409 AC XY: 139AN XY: 34008
GnomAD3 exomes AF: 0.00422 AC: 771AN: 182742Hom.: 1 AF XY: 0.00428 AC XY: 288AN XY: 67270
GnomAD4 exome AF: 0.00765 AC: 8402AN: 1097921Hom.: 29 Cov.: 32 AF XY: 0.00720 AC XY: 2615AN XY: 363309
GnomAD4 genome AF: 0.00478 AC: 535AN: 111889Hom.: 2 Cov.: 23 AF XY: 0.00408 AC XY: 139AN XY: 34073
ClinVar
Submissions by phenotype
not provided Benign:1
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Polyagglutinable erythrocyte syndrome Benign:1
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C1GALT1C1-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