Variant rs13385681 details in Genebe, Genetics Data Aggregator

Variant summary

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

The 2-100470432-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,388,972 control chromosomes in the GnomAD database, including 34,381 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 0.24 ( 4441 hom., cov: 32)

Exomes 𝑓: 0.22 ( 29940 hom. )

Consequence

NMS
ENST00000376865.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

Variant links:

Genes affected

NMS (HGNC:32203): (neuromedin S) This gene encodes a member of the neuromedin family of neuropeptides. The encoded preproprotein is proteolytically processed to generate a biologically active neuropeptide that plays a role in the regulation of circadian rhythm, anorexigenic action, antidiuretic action, cardiovascular function and stimulation of oxytocin and vasopressin release. [provided by RefSeq, May 2016]

NMS links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NMS	NM_001011717.1 linkuse as main transcript			upstream_gene_variant		ENST00000376865.1	NP_001011717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NMS	ENST00000376865.1 linkuse as main transcript			upstream_gene_variant		1	NM_001011717.1	ENSP00000366061	P1

Frequencies

GnomAD3 genomes

AF:

0.236

AC:

35824

AN:

151882

Hom.:

4443

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.205

GnomAD4 exome

AF:

0.217

AC:

268720

AN:

1236972

Hom.:

29940

Cov.:

AF XY:

0.219

AC XY:

137612

AN XY:

627110

show subpopulations

Gnomad4 AFR exome

AF:

0.257

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.320

Gnomad4 SAS exome

AF:

0.279

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.236

AC:

35833

AN:

152000

Hom.:

4441

Cov.:

AF XY:

0.237

AC XY:

17575

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.347

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.229

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.204

Alfa

AF:

0.216

Hom.:

3498

Bravo

AF:

0.234

Asia WGS

AF:

0.289

AC:

1005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.9

DANN

Benign

0.49

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over