rs188395796
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000751.3(CHRND):c.1371+7G>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 0.000761 in 1,612,874 control chromosomes in the GnomAD database, including 3 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_000751.3 splice_region, 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 |
---|---|---|---|---|---|---|---|
CHRND | NM_000751.3 | c.1371+7G>T | splice_region_variant, intron_variant | ENST00000258385.8 | |||
CHRND | NM_001256657.2 | c.1326+7G>T | splice_region_variant, intron_variant | ||||
CHRND | NM_001311195.2 | c.789+7G>T | splice_region_variant, intron_variant | ||||
CHRND | NM_001311196.2 | c.1068+7G>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRND | ENST00000258385.8 | c.1371+7G>T | splice_region_variant, intron_variant | 1 | NM_000751.3 | P1 | |||
CHRND | ENST00000543200.5 | c.1326+7G>T | splice_region_variant, intron_variant | 2 | |||||
CHRND | ENST00000441621.6 | c.*553+7G>T | splice_region_variant, intron_variant, NMD_transcript_variant | 5 | |||||
CHRND | ENST00000446616.1 | c.*1012+7G>T | splice_region_variant, intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00328 AC: 500AN: 152214Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000935 AC: 235AN: 251434Hom.: 0 AF XY: 0.000692 AC XY: 94AN XY: 135888
GnomAD4 exome AF: 0.000498 AC: 728AN: 1460542Hom.: 0 Cov.: 31 AF XY: 0.000465 AC XY: 338AN XY: 726666
GnomAD4 genome AF: 0.00328 AC: 500AN: 152332Hom.: 3 Cov.: 33 AF XY: 0.00302 AC XY: 225AN XY: 74490
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 03, 2016 | - - |
Lethal multiple pterygium syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CHRND: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at