chr11-92984997-A-T

Variant names:

• chr11-92984997-A-T
• rs1447351
• ENST00000528076.1:c.*16A>T

Variant summary

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

The ENST00000528076.1(MTNR1B):​c.*16A>T variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MTNR1B ENST00000528076.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 12 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 (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTNR1B	XM_011542839.3	c.*602A>T		downstream_gene_variant			XP_011541141.1
MTNR1B	XM_017017777.2	c.*602A>T		downstream_gene_variant			XP_016873266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTNR1B	ENST00000528076.1	c.*16A>T		3_prime_UTR_variant	Exon 2 of 2	3		ENSP00000433573.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 299480 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 170662

African (AFR) AF: 0.00 AC: 0 AN: 8486

American (AMR) AF: 0.00 AC: 0 AN: 26948

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10378

East Asian (EAS) AF: 0.00 AC: 0 AN: 9190

South Asian (SAS) AF: 0.00 AC: 0 AN: 58786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12192

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2738

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 156744

Other (OTH) AF: 0.00 AC: 0 AN: 14018

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.79
PhyloP100		-0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1447351; hg19: chr11-92718163;