chr5-177600185-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_007255.3(B4GALT7):c.-26C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,342,070 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007255.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B4GALT7 | NM_007255.3 | c.-26C>T | 5_prime_UTR_variant | Exon 1 of 6 | ENST00000029410.10 | NP_009186.1 | ||
B4GALT7 | XM_047416681.1 | c.-1136C>T | 5_prime_UTR_variant | Exon 1 of 7 | XP_047272637.1 | |||
B4GALT7 | XM_047416682.1 | c.-421C>T | 5_prime_UTR_variant | Exon 1 of 7 | XP_047272638.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00212 AC: 321AN: 151620Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00161 AC: 71AN: 43976Hom.: 0 AF XY: 0.00195 AC XY: 51AN XY: 26202
GnomAD4 exome AF: 0.00369 AC: 4387AN: 1190342Hom.: 10 Cov.: 30 AF XY: 0.00364 AC XY: 2114AN XY: 580118
GnomAD4 genome AF: 0.00212 AC: 321AN: 151728Hom.: 1 Cov.: 32 AF XY: 0.00222 AC XY: 165AN XY: 74158
ClinVar
Submissions by phenotype
not specified Benign:1
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:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at