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GeneBe

rs10830963

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005959.5(MTNR1B):c.223+5596C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,102 control chromosomes in the GnomAD database, including 4,987 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 0.23 ( 4987 hom., cov: 33)

Consequence

MTNR1B
NM_005959.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTNR1BNM_005959.5 linkuse as main transcriptc.223+5596C>G intron_variant ENST00000257068.3
MTNR1BXM_011542839.3 linkuse as main transcriptc.223+5596C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTNR1BENST00000257068.3 linkuse as main transcriptc.223+5596C>G intron_variant 1 NM_005959.5 P1
MTNR1BENST00000528076.1 linkuse as main transcriptc.165+5596C>G intron_variant 3
MTNR1BENST00000532482.1 linkuse as main transcriptc.*114+2953C>G intron_variant, NMD_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.230
AC:
34989
AN:
151984
Hom.:
4993
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0688
Gnomad AMI
AF:
0.469
Gnomad AMR
AF:
0.221
Gnomad ASJ
AF:
0.234
Gnomad EAS
AF:
0.433
Gnomad SAS
AF:
0.414
Gnomad FIN
AF:
0.353
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.241
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.230
AC:
34984
AN:
152102
Hom.:
4987
Cov.:
33
AF XY:
0.237
AC XY:
17624
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.0686
Gnomad4 AMR
AF:
0.220
Gnomad4 ASJ
AF:
0.234
Gnomad4 EAS
AF:
0.433
Gnomad4 SAS
AF:
0.414
Gnomad4 FIN
AF:
0.353
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.277
Hom.:
3538
Bravo
AF:
0.211
Asia WGS
AF:
0.345
AC:
1200
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
5.2
Dann
Benign
0.43

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: rs10830963; hg19: chr11-92708710; API