chr22-40679691-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05
Variant links:
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
MCHR1NM_005297.4 linkuse as main transcriptc.39C>T p.Asn13= synonymous_variant 1/2 ENST00000249016.5 NP_005288.4
LOC124905123XR_007068110.1 linkuse as main transcriptn.358+917G>A intron_variant, non_coding_transcript_variant
LOC124905123XR_007068109.1 linkuse as main transcriptn.4323+917G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MCHR1ENST00000249016.5 linkuse as main transcriptc.39C>T p.Asn13= synonymous_variant 1/21 NM_005297.4 ENSP00000249016 P1
MCHR1ENST00000381433.3 linkuse as main transcriptc.39C>T p.Asn13= synonymous_variant 1/31 ENSP00000370841
MCHR1ENST00000498400.1 linkuse as main transcriptn.132+287C>T intron_variant, non_coding_transcript_variant 1
ENST00000688408.2 linkuse as main transcriptn.367+917G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.600
AC:
91089
AN:
151800
Hom.:
27989
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.578
Gnomad AMI
AF:
0.546
Gnomad AMR
AF:
0.470
Gnomad ASJ
AF:
0.565
Gnomad EAS
AF:
0.978
Gnomad SAS
AF:
0.469
Gnomad FIN
AF:
0.664
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.616
Gnomad OTH
AF:
0.591
GnomAD3 exomes
AF:
0.588
AC:
146332
AN:
249066
Hom.:
46182
AF XY:
0.589
AC XY:
79445
AN XY:
134866
show subpopulations
Gnomad AFR exome
AF:
0.577
Gnomad AMR exome
AF:
0.345
Gnomad ASJ exome
AF:
0.556
Gnomad EAS exome
AF:
0.982
Gnomad SAS exome
AF:
0.454
Gnomad FIN exome
AF:
0.672
Gnomad NFE exome
AF:
0.623
Gnomad OTH exome
AF:
0.573
GnomAD4 exome
AF:
0.603
AC:
881558
AN:
1461698
Hom.:
272469
Cov.:
65
AF XY:
0.601
AC XY:
436890
AN XY:
727168
show subpopulations
Gnomad4 AFR exome
AF:
0.572
Gnomad4 AMR exome
AF:
0.364
Gnomad4 ASJ exome
AF:
0.550
Gnomad4 EAS exome
AF:
0.990
Gnomad4 SAS exome
AF:
0.455
Gnomad4 FIN exome
AF:
0.671
Gnomad4 NFE exome
AF:
0.610
Gnomad4 OTH exome
AF:
0.599
GnomAD4 genome
AF:
0.600
AC:
91148
AN:
151918
Hom.:
28010
Cov.:
31
AF XY:
0.600
AC XY:
44535
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.469
Gnomad4 ASJ
AF:
0.565
Gnomad4 EAS
AF:
0.977
Gnomad4 SAS
AF:
0.469
Gnomad4 FIN
AF:
0.664
Gnomad4 NFE
AF:
0.616
Gnomad4 OTH
AF:
0.597
Alfa
AF:
0.582
Hom.:
17693
Bravo
AF:
0.587
Asia WGS
AF:
0.691
AC:
2399
AN:
3478
EpiCase
AF:
0.607
EpiControl
AF:
0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
2.6
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs133073; hg19: chr22-41075695; COSMIC: COSV50760998; COSMIC: COSV50760998; API