chr1-37540758-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024700.4(SNIP1):c.328-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 1,578,512 control chromosomes in the GnomAD database, including 556,525 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_024700.4 splice_region, splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNIP1 | NM_024700.4 | c.328-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000296215.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNIP1 | ENST00000296215.8 | c.328-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024700.4 | P1 | |||
SNIP1 | ENST00000638725.1 | n.837T>C | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
SNIP1 | ENST00000468040.2 | c.*102-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.747 AC: 113480AN: 152002Hom.: 44708 Cov.: 32
GnomAD3 exomes AF: 0.820 AC: 191782AN: 233950Hom.: 80345 AF XY: 0.818 AC XY: 103961AN XY: 127088
GnomAD4 exome AF: 0.843 AC: 1203034AN: 1426394Hom.: 511782 Cov.: 40 AF XY: 0.840 AC XY: 592217AN XY: 705402
GnomAD4 genome AF: 0.747 AC: 113562AN: 152118Hom.: 44743 Cov.: 32 AF XY: 0.749 AC XY: 55723AN XY: 74380
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Psychomotor retardation, epilepsy, and craniofacial dysmorphism Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at