4-56490564-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_006947.4(SRP72):c.1425-4T>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 0.000443 in 1,613,164 control chromosomes in the GnomAD database, including 8 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_006947.4 splice_region, splice_polypyrimidine_tract, 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 |
---|---|---|---|---|---|---|---|
SRP72 | NM_006947.4 | c.1425-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000642900.1 | |||
SRP72 | NM_001267722.2 | c.1242-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SRP72 | XM_024454192.2 | c.1425-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SRP72 | NR_151856.2 | n.1444-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRP72 | ENST00000642900.1 | c.1425-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_006947.4 | P1 | ||||
SRP72 | ENST00000510663.6 | c.1242-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SRP72 | ENST00000646579.1 | n.436-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||||
SRP72 | ENST00000647432.1 | n.527-4T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 337AN: 152210Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000617 AC: 154AN: 249730Hom.: 3 AF XY: 0.000548 AC XY: 74AN XY: 134994
GnomAD4 exome AF: 0.000257 AC: 375AN: 1460836Hom.: 5 Cov.: 30 AF XY: 0.000233 AC XY: 169AN XY: 726666
GnomAD4 genome AF: 0.00223 AC: 339AN: 152328Hom.: 3 Cov.: 33 AF XY: 0.00200 AC XY: 149AN XY: 74488
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 22, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at