rs11739167

chr5-25909655-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511640.1(MSNP1):n.153C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,600,550 control chromosomes in the GnomAD database, including 162,027 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 0.48 (17795 hom., cov: 31)
  • Exomes 𝑓: 0.44 (144232 hom.)
• Consequence: MSNP1 ENST00000511640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

MSNP1 (HGNC:7374): (moesin pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSNP1	ENST00000511640.1	n.153C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72628 AN: 151688 Hom.: 17783 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.443 AC: 641247 AN: 1448744 Hom.: 144232 Cov.: 48 AF XY: 0.445 AC XY: 320639 AN XY: 721006

Gnomad4 AFR exome AF: 0.567

Gnomad4 AMR exome AF: 0.416

Gnomad4 ASJ exome AF: 0.369

Gnomad4 EAS exome AF: 0.558

Gnomad4 SAS exome AF: 0.499

Gnomad4 FIN exome AF: 0.418

Gnomad4 NFE exome AF: 0.434

Gnomad4 OTH exome AF: 0.449

GnomAD4 genome AF: 0.479 AC: 72684 AN: 151806 Hom.: 17795 Cov.: 31 AF XY: 0.479 AC XY: 35570 AN XY: 74186

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.454

Alfa AF: 0.443 Hom.: 5408

Bravo AF: 0.480

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	2.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11739167; hg19: chr5-25909764;