rs10830963

Variant names:

• chr11-92975544-C-G
• rs10830963
• NM_005959.5:c.223+5596C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-92975544-C-G
• chr11-92975544-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 609 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
MTNR1B	NM_005959.5	c.223+5596C>G		intron_variant	Intron 1 of 1	ENST00000257068.3	NP_005950.1
MTNR1B	XM_011542839.3	c.223+5596C>G		intron_variant	Intron 1 of 2		XP_011541141.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTNR1B	ENST00000257068.3	c.223+5596C>G		intron_variant	Intron 1 of 1	1	NM_005959.5	ENSP00000257068.2
MTNR1B	ENST00000528076.1	c.164+5596C>G		intron_variant	Intron 1 of 1	3		ENSP00000433573.1
MTNR1B	ENST00000532482.1	n.*114+2953C>G		intron_variant	Intron 2 of 2	5		ENSP00000436101.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34989 AN: 151984 Hom.: 4993 Cov.: 33

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

African (AFR) AF: 0.0686 AC: 2850 AN: 41532

American (AMR) AF: 0.220 AC: 3366 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2239 AN: 5166

South Asian (SAS) AF: 0.414 AC: 1988 AN: 4806

European-Finnish (FIN) AF: 0.353 AC: 3724 AN: 10546

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18985 AN: 67984

Other (OTH) AF: 0.241 AC: 510 AN: 2116

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
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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: rs10830963; hg19: chr11-92708710;