chr22-40679691-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005297.4(MCHR1):c.39C>T(p.Asn13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 1,613,616 control chromosomes in the GnomAD database, including 300,479 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.60 ( 28010 hom., cov: 31)
Exomes 𝑓: 0.60 ( 272469 hom. )
Consequence
MCHR1
NM_005297.4 synonymous
NM_005297.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP7
Synonymous conserved (PhyloP=-1.05 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCHR1 | NM_005297.4 | c.39C>T | p.Asn13= | synonymous_variant | 1/2 | ENST00000249016.5 | NP_005288.4 | |
LOC124905123 | XR_007068110.1 | n.358+917G>A | intron_variant, non_coding_transcript_variant | |||||
LOC124905123 | XR_007068109.1 | n.4323+917G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCHR1 | ENST00000249016.5 | c.39C>T | p.Asn13= | synonymous_variant | 1/2 | 1 | NM_005297.4 | ENSP00000249016 | P1 | |
MCHR1 | ENST00000381433.3 | c.39C>T | p.Asn13= | synonymous_variant | 1/3 | 1 | ENSP00000370841 | |||
MCHR1 | ENST00000498400.1 | n.132+287C>T | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000688408.2 | n.367+917G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.600 AC: 91089AN: 151800Hom.: 27989 Cov.: 31
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GnomAD3 exomes AF: 0.588 AC: 146332AN: 249066Hom.: 46182 AF XY: 0.589 AC XY: 79445AN XY: 134866
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GnomAD4 exome AF: 0.603 AC: 881558AN: 1461698Hom.: 272469 Cov.: 65 AF XY: 0.601 AC XY: 436890AN XY: 727168
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GnomAD4 genome AF: 0.600 AC: 91148AN: 151918Hom.: 28010 Cov.: 31 AF XY: 0.600 AC XY: 44535AN XY: 74226
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at