22-40679519-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005297.4(MCHR1):c.-134C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,613,944 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00094 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 4 hom. )
Consequence
MCHR1
NM_005297.4 5_prime_UTR
NM_005297.4 5_prime_UTR
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 0.160
Genes affected
MCHR1 (HGNC:4479): (melanin concentrating hormone receptor 1) The protein encoded by this gene, a member of the G protein-coupled receptor family 1, is an integral plasma membrane protein which binds melanin-concentrating hormone. The encoded protein can inhibit cAMP accumulation and stimulate intracellular calcium flux, and is probably involved in the neuronal regulation of food consumption. Although structurally similar to somatostatin receptors, this protein does not seem to bind somatostatin. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0060786903).
BP6
Variant 22-40679519-C-T is Benign according to our data. Variant chr22-40679519-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3042319.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-40679519-C-T is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCHR1 | NM_005297.4 | c.-134C>T | 5_prime_UTR_variant | 1/2 | ENST00000249016.5 | ||
LOC124905123 | XR_007068110.1 | n.358+1089G>A | intron_variant, non_coding_transcript_variant | ||||
LOC124905123 | XR_007068109.1 | n.4323+1089G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCHR1 | ENST00000249016.5 | c.-134C>T | 5_prime_UTR_variant | 1/2 | 1 | NM_005297.4 | P1 | ||
MCHR1 | ENST00000381433.3 | c.-134C>T | 5_prime_UTR_variant | 1/3 | 1 | ||||
MCHR1 | ENST00000498400.1 | n.132+115C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
ENST00000688408.2 | n.367+1089G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000940 AC: 143AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000885 AC: 221AN: 249660Hom.: 1 AF XY: 0.000910 AC XY: 123AN XY: 135234
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GnomAD4 exome AF: 0.00113 AC: 1651AN: 1461640Hom.: 4 Cov.: 31 AF XY: 0.00118 AC XY: 859AN XY: 727118
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GnomAD4 genome AF: 0.000939 AC: 143AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000953 AC XY: 71AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MCHR1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 25, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at