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

Genomes: 𝑓 0.00044 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 0 hom. )

Consequence

CHMP1A
NM_001083314.4 missense

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: 0.838
Variant links:
Genes affected
CHMP1A (HGNC:8740): (charged multivesicular body protein 1A) This gene encodes a member of the CHMP/Chmp family of proteins which are involved in multivesicular body sorting of proteins to the interiors of lysosomes. The initial prediction of the protein sequence encoded by this gene suggested that the encoded protein was a metallopeptidase. The nomenclature has been updated recently to reflect the correct biological function of this encoded protein. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 16-89646688-G-A is Benign according to our data. Variant chr16-89646688-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 390042.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Uncertain_significance=1}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00044 (67/152188) while in subpopulation NFE AF= 0.000661 (45/68034). AF 95% confidence interval is 0.000508. There are 0 homozygotes in gnomad4. There are 35 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHMP1ANM_002768.5 linkc.408C>T p.Ala136Ala synonymous_variant Exon 6 of 7 ENST00000397901.8 NP_002759.2 Q9HD42-1
CHMP1ANM_001083314.4 linkc.388C>T p.His130Tyr missense_variant Exon 5 of 6 NP_001076783.1
CHMP1AXM_047434195.1 linkc.216C>T p.Ala72Ala synonymous_variant Exon 6 of 7 XP_047290151.1
CHMP1ANR_046418.3 linkn.696C>T non_coding_transcript_exon_variant Exon 6 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHMP1AENST00000397901.8 linkc.408C>T p.Ala136Ala synonymous_variant Exon 6 of 7 1 NM_002768.5 ENSP00000380998.3 Q9HD42-1

Frequencies

GnomAD3 genomes
AF:
0.000440
AC:
67
AN:
152188
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000661
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000320
AC:
77
AN:
240492
Hom.:
0
AF XY:
0.000290
AC XY:
38
AN XY:
131174
show subpopulations
Gnomad AFR exome
AF:
0.000347
Gnomad AMR exome
AF:
0.000147
Gnomad ASJ exome
AF:
0.000204
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000241
Gnomad NFE exome
AF:
0.000544
Gnomad OTH exome
AF:
0.000171
GnomAD4 exome
AF:
0.000325
AC:
474
AN:
1458048
Hom.:
0
Cov.:
33
AF XY:
0.000321
AC XY:
233
AN XY:
724954
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.000203
Gnomad4 ASJ exome
AF:
0.000192
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000211
Gnomad4 NFE exome
AF:
0.000387
Gnomad4 OTH exome
AF:
0.000183
GnomAD4 genome
AF:
0.000440
AC:
67
AN:
152188
Hom.:
0
Cov.:
33
AF XY:
0.000471
AC XY:
35
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.000314
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.000661
Gnomad4 OTH
AF:
0.00143
Alfa
AF:
0.000479
Hom.:
0
Bravo
AF:
0.000385

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Benign:2
Oct 16, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 03, 2019
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Inborn genetic diseases Uncertain:1
Jan 26, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
Jan 27, 2017
Genetic Services Laboratory, University of Chicago
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
13
DANN
Benign
0.88
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61730919; hg19: chr16-89713096; API