5-25909655-C-T

Variant names:

• chr5-25909655-C-T
• rs11739167
• ENST00000511640.1:n.153C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511640.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSNP1	ENST00000511640.1	TSL:6	n.153C>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.567 AC: 18835 AN: 33196

American (AMR) AF: 0.416 AC: 18499 AN: 44508

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 9603 AN: 25990

East Asian (EAS) AF: 0.558 AC: 22046 AN: 39512

South Asian (SAS) AF: 0.499 AC: 42908 AN: 85994

European-Finnish (FIN) AF: 0.418 AC: 22180 AN: 53034

Middle Eastern (MID) AF: 0.412 AC: 2360 AN: 5730

European-Non Finnish (NFE) AF: 0.434 AC: 477997 AN: 1100994

Other (OTH) AF: 0.449 AC: 26819 AN: 59786

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

African (AFR) AF: 0.569 AC: 23539 AN: 41346

American (AMR) AF: 0.443 AC: 6768 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3050 AN: 5124

South Asian (SAS) AF: 0.505 AC: 2426 AN: 4804

European-Finnish (FIN) AF: 0.431 AC: 4537 AN: 10528

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29708 AN: 67952

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.440 Hom.: 6128

Bravo AF: 0.480

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs11739167; hg19: chr5-25909764;