chr4-71763401-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000583.4(GC):c.701+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000328 in 1,486,050 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000583.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GC | NM_000583.4 | c.701+7A>G | splice_region_variant, intron_variant | ENST00000273951.13 | |||
GC | NM_001204306.1 | c.701+7A>G | splice_region_variant, intron_variant | ||||
GC | NM_001204307.1 | c.758+7A>G | splice_region_variant, intron_variant | ||||
GC | XM_006714177.3 | c.701+7A>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GC | ENST00000273951.13 | c.701+7A>G | splice_region_variant, intron_variant | 1 | NM_000583.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000494 AC: 123AN: 249174Hom.: 1 AF XY: 0.000520 AC XY: 70AN XY: 134662
GnomAD4 exome AF: 0.000336 AC: 448AN: 1333756Hom.: 2 Cov.: 20 AF XY: 0.000374 AC XY: 251AN XY: 670772
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at