rs9568169

chr13-49220514-C-Achr13-49220514-C-Gchr13-49220514-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001507.1(MLNR):c.177C>A(p.Thr59=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,603,658 control chromosomes in the GnomAD database, including 85,173 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 0.31 (7710 hom., cov: 32)
  • Exomes 𝑓: 0.32 (77463 hom.)
• Consequence: MLNR NM_001507.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

MLNR (HGNC:4495): (motilin receptor) Motilin is a 22 amino acid peptide hormone expressed throughout the gastrointestinal (GI) tract. The protein encoded by this gene is a motilin receptor which is a member of the G-protein coupled receptor 1 family. This member is a multi-pass transmembrane protein, and is an important therapeutic target for the treatment of hypomotility disorders. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BP7: Synonymous conserved (PhyloP=-0.932 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLNR	NM_001507.1	c.177C>A	p.Thr59=	synonymous_variant	1/2	ENST00000218721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLNR	ENST00000218721.1	c.177C>A	p.Thr59=	synonymous_variant	1/2	1	NM_001507.1	P1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47852 AN: 151844 Hom.: 7704 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.324

GnomAD3 exomes AF: 0.344 AC: 78189 AN: 227320 Hom.: 13817 AF XY: 0.353 AC XY: 43462 AN XY: 123286

Gnomad AFR exome AF: 0.289

Gnomad AMR exome AF: 0.321

Gnomad ASJ exome AF: 0.339

Gnomad EAS exome AF: 0.462

Gnomad SAS exome AF: 0.492

Gnomad FIN exome AF: 0.300

Gnomad NFE exome AF: 0.307

Gnomad OTH exome AF: 0.320

GnomAD4 exome AF: 0.321 AC: 466694 AN: 1451696 Hom.: 77463 Cov.: 38 AF XY: 0.327 AC XY: 235923 AN XY: 721426

Gnomad4 AFR exome AF: 0.282

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.493

Gnomad4 SAS exome AF: 0.489

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.305

Gnomad4 OTH exome AF: 0.324

GnomAD4 genome AF: 0.315 AC: 47858 AN: 151962 Hom.: 7710 Cov.: 32 AF XY: 0.318 AC XY: 23609 AN XY: 74266

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.321

Alfa AF: 0.305 Hom.: 8894

Bravo AF: 0.310

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	1.4
Dann	Benign	0.88

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

Other links and lift over

dbSNP: rs9568169; hg19: chr13-49794650; COSMIC: COSV54532305;