chr11-92969849-G-A

Variant names:

• chr11-92969849-G-A
• rs387906779
• NM_005959.5:c.124G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005959.5(MTNR1B):​c.124G>A​(p.Ala42Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A42P) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MTNR1B NM_005959.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 4 publications found

Genes affected

MTNR1B (HGNC:7464): (melatonin receptor 1B) This gene encodes one of two high affinity forms of a receptor for melatonin, the primary hormone secreted by the pineal gland. This gene product is an integral membrane protein that is a G-protein coupled, 7-transmembrane receptor. It is found primarily in the retina and brain although this detection requires RT-PCR. It is thought to participate in light-dependent functions in the retina and may be involved in the neurobiological effects of melatonin. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05351296).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTNR1B	NM_005959.5	c.124G>A	p.Ala42Thr	missense_variant	Exon 1 of 2	ENST00000257068.3	NP_005950.1
MTNR1B	XM_011542839.3	c.124G>A	p.Ala42Thr	missense_variant	Exon 1 of 3		XP_011541141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTNR1B	ENST00000257068.3	c.124G>A	p.Ala42Thr	missense_variant	Exon 1 of 2	1	NM_005959.5	ENSP00000257068.2
MTNR1B	ENST00000528076.1	c.65G>A	p.Ser22Asn	missense_variant	Exon 1 of 2	3		ENSP00000433573.1
MTNR1B	ENST00000532482.1	n.124G>A		non_coding_transcript_exon_variant	Exon 1 of 3	5		ENSP00000436101.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.34	T
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.2
DANN	Benign	0.86
DEOGEN2	Benign	0.064	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.057	N
LIST_S2	Benign	0.76	T
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L
PhyloP100		0.025
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-0.59	N
REVEL	Benign	0.0090
Sift	Benign	0.68	T
Sift4G	Benign	0.52	T
Polyphen		0.0090	B
Vest4		0.14
MutPred		0.39		Gain of glycosylation at A42 (P = 0.0726);
MVP		0.31
MPC		0.15
ClinPred		0.19	T
GERP RS		-1.1
PromoterAI		0.037	Neutral
Varity_R		0.023
gMVP		0.38
Mutation Taster		=92/8	polymorphism

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

Other links and lift over

dbSNP: rs387906779; hg19: chr11-92703015;