Variant 6-99934404-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001040179.2(MCHR2):c.701C>A(p.Ala234Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000408 in 1,420,884 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000041 ( 0 hom. )

Consequence

MCHR2
NM_001040179.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.86

Variant links:

Genes affected

MCHR2 (HGNC:20867): (melanin concentrating hormone receptor 2) Predicted to enable G protein-coupled peptide receptor activity. Predicted to be involved in neuropeptide signaling pathway. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MCHR2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
MCHR2	NM_001040179.2 linkuse as main transcript	c.701C>A	p.Ala234Asp	missense_variant	5/6	ENST00000281806.7	NP_001035269.1
MCHR2	NM_032503.3 linkuse as main transcript	c.701C>A	p.Ala234Asp	missense_variant	5/6		NP_115892.2
MCHR2	XM_024446571.2 linkuse as main transcript	c.701C>A	p.Ala234Asp	missense_variant	5/6		XP_024302339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MCHR2	ENST00000281806.7 linkuse as main transcript	c.701C>A	p.Ala234Asp	missense_variant	5/6	2	NM_001040179.2	ENSP00000281806	P1
MCHR2	ENST00000369212.2 linkuse as main transcript	c.701C>A	p.Ala234Asp	missense_variant	5/6	1		ENSP00000358214	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000184

AC:

AN:

216924

Hom.:

AF XY:

0.0000255

AC XY:

AN XY:

117876

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000387

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000408

AC:

AN:

1420884

Hom.:

Cov.:

AF XY:

0.0000354

AC XY:

AN XY:

706284

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0000409

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000519

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ExAC

AF:

0.0000247

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 03, 2024

The c.701C>A (p.A234D) alteration is located in exon 5 (coding exon 4) of the MCHR2 gene. This alteration results from a C to A substitution at nucleotide position 701, causing the alanine (A) at amino acid position 234 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.015

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.29

T;T

Eigen

Benign

-0.14

Eigen_PC

Benign

-0.022

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.49

T;.

M_CAP

Benign

0.011

MetaRNN

Uncertain

0.50

T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.9

L;L

MutationTaster

Benign

0.80

D;D;D

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-2.8

D;D

REVEL

Uncertain

0.38

Sift

Uncertain

0.0090

D;D

Sift4G

Uncertain

0.039

D;D

Polyphen

0.25

B;B

Vest4

0.44

MutPred

0.61

Gain of disorder (P = 0.0291);Gain of disorder (P = 0.0291);

MVP

0.90

MPC

0.23

ClinPred

0.81

GERP RS

4.2

Varity_R

0.35

gMVP

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over