chr8-41612000-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_178819.4(GPAT4):c.701+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,613,684 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_178819.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPAT4 | NM_178819.4 | c.701+8C>T | splice_region_variant, intron_variant | ENST00000396987.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPAT4 | ENST00000396987.7 | c.701+8C>T | splice_region_variant, intron_variant | 1 | NM_178819.4 | P1 | |||
ENST00000581909.1 | n.547-2126G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00135 AC: 205AN: 152140Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00292 AC: 733AN: 250834Hom.: 8 AF XY: 0.00376 AC XY: 510AN XY: 135596
GnomAD4 exome AF: 0.00147 AC: 2146AN: 1461426Hom.: 30 Cov.: 31 AF XY: 0.00204 AC XY: 1482AN XY: 727028
GnomAD4 genome AF: 0.00135 AC: 206AN: 152258Hom.: 3 Cov.: 33 AF XY: 0.00180 AC XY: 134AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at