dbSNP rs9611386: MCHR1:c.*601A>G (chr22-40682529-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005297.4(MCHR1):c.*601A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0964 in 158,318 control chromosomes in the GnomAD database, including 1,091 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 0.099 ( 1080 hom., cov: 31)

Exomes 𝑓: 0.045 ( 11 hom. )

Consequence

MCHR1
NM_005297.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.185

Publications

9 publications found

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]

MCHR1 links:

ENSG00000289292 (HGNC:):

ENSG00000289292 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MCHR1	NM_005297.4 link	c.*601A>G	3_prime_UTR_variant	Exon 2 of 2	ENST00000249016.5	NP_005288.4	Q99705
LOC124905123	XR_007068109.1 link	n.2402T>C	non_coding_transcript_exon_variant	Exon 1 of 2
LOC124905123	XR_007068110.1 link	n.189-1752T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCHR1	ENST00000249016.5 link	c.*601A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_005297.4	ENSP00000249016.5		Q99705

Frequencies

GnomAD3 genomes

AF:

0.0985

AC:

14971

AN:

151998

Hom.:

1077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0779

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.0875

Gnomad FIN

AF:

0.0254

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0575

Gnomad OTH

AF:

0.0742

GnomAD4 exome

AF:

0.0445

AC:

276

AN:

6202

Hom.:

Cov.:

AF XY:

0.0471

AC XY:

155

AN XY:

3290

show subpopulations

African (AFR)

AF:

0.0385

AC:

AN:

American (AMR)

AF:

0.0385

AC:

AN:

1560

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.0705

AC:

AN:

312

South Asian (SAS)

AF:

0.0380

AC:

AN:

552

European-Finnish (FIN)

AF:

0.0216

AC:

AN:

464

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0499

AC:

153

AN:

3068

Other (OTH)

AF:

0.0455

AC:

AN:

198

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.524

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0985

AC:

14988

AN:

152116

Hom.:

1080

Cov.:

AF XY:

0.0966

AC XY:

7187

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.198

AC:

8199

AN:

41460

American (AMR)

AF:

0.0778

AC:

1189

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3468

East Asian (EAS)

AF:

0.132

AC:

683

AN:

5174

South Asian (SAS)

AF:

0.0873

AC:

420

AN:

4810

European-Finnish (FIN)

AF:

0.0254

AC:

270

AN:

10612

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0575

AC:

3913

AN:

68000

Other (OTH)

AF:

0.0739

AC:

156

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

656

1312

1969

2625

3281

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0735

Hom.:

1288

Bravo

AF:

0.104

Asia WGS

AF:

0.0980

AC:

341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.4

(source)

DANN

Benign

0.86

PhyloP100

0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over