rs376134678
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152594.3(SPRED1):c.377-10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000557 in 1,599,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_152594.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPRED1 | ENST00000299084.9 | c.377-10A>G | intron_variant | Intron 3 of 6 | 1 | NM_152594.3 | ENSP00000299084.4 | |||
SPRED1 | ENST00000561317.1 | c.314-10A>G | intron_variant | Intron 4 of 5 | 4 | ENSP00000453680.1 | ||||
SPRED1 | ENST00000561205.1 | n.715-10A>G | intron_variant | Intron 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000432 AC: 10AN: 231320Hom.: 0 AF XY: 0.0000641 AC XY: 8AN XY: 124824
GnomAD4 exome AF: 0.0000373 AC: 54AN: 1446746Hom.: 0 Cov.: 29 AF XY: 0.0000404 AC XY: 29AN XY: 718462
GnomAD4 genome AF: 0.000230 AC: 35AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:2
377-10A>G in intron 3 of SPRED1: This variant has been identified by our labora tory in a proband and an unaffected parent. This variant is located in the 3' sp lice acceptor region but does not affect the invariant -1 and -2 positions. In a ddition, computational tools do not predict altered splicing. This variant has b een identified in 0.05% (2/4392) of African American chromosomes from a large po pulation by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS /). In addition, the adenine nucleotide is not conserved across evolutionary dis tinct species at position 377-10, and several mammals have a guanine at this pos ition. Therefore, the 377-10A>G variant is likely to be benign. -
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not provided Benign:1
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Legius syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at