rs61730919
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001083314.4(CHMP1A):c.388C>T(p.His130Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000336 in 1,610,236 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001083314.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHMP1A | NM_002768.5 | c.408C>T | p.Ala136Ala | synonymous_variant | Exon 6 of 7 | ENST00000397901.8 | NP_002759.2 | |
CHMP1A | NM_001083314.4 | c.388C>T | p.His130Tyr | missense_variant | Exon 5 of 6 | NP_001076783.1 | ||
CHMP1A | XM_047434195.1 | c.216C>T | p.Ala72Ala | synonymous_variant | Exon 6 of 7 | XP_047290151.1 | ||
CHMP1A | NR_046418.3 | n.696C>T | non_coding_transcript_exon_variant | Exon 6 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000320 AC: 77AN: 240492Hom.: 0 AF XY: 0.000290 AC XY: 38AN XY: 131174
GnomAD4 exome AF: 0.000325 AC: 474AN: 1458048Hom.: 0 Cov.: 33 AF XY: 0.000321 AC XY: 233AN XY: 724954
GnomAD4 genome AF: 0.000440 AC: 67AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.000471 AC XY: 35AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:2
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Inborn genetic diseases Uncertain:1
The c.388C>T (p.H130Y) alteration is located in exon 5 (coding exon 5) of the CHMP1A gene. This alteration results from a C to T substitution at nucleotide position 388, causing the histidine (H) at amino acid position 130 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at