rs1332720

chrX-65595656-C-T

Variant summary

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

The ENST00000609205.5(MSN):n.539+5887C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 112,042 control chromosomes in the GnomAD database, including 7,495 homozygotes. There are 7,382 hemizygotes in GnomAD. 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 (7495 hom., 7382 hem., cov: 23)
• Consequence: MSN ENST00000609205.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

MSN (HGNC:7373): (moesin) Moesin (for membrane-organizing extension spike protein) is a member of the ERM family which includes ezrin and radixin. ERM proteins appear to function as cross-linkers between plasma membranes and actin-based cytoskeletons. Moesin is localized to filopodia and other membranous protrusions that are important for cell-cell recognition and signaling and for cell movement. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSN	XM_005262269.3	c.15+7044C>T		intron_variant
MSN	XM_011530959.1	c.111+6588C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSN	ENST00000609205.5	n.539+5887C>T		intron_variant, non_coding_transcript_variant		1
MSN	ENST00000609672.5	c.-22+7044C>T		intron_variant		4
MSN	ENST00000429601.1	n.399-5006C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.236 AC: 26409 AN: 111992 Hom.: 7487 Cov.: 23 AF XY: 0.215 AC XY: 7338 AN XY: 34168

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.00604

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.00258

Gnomad MID AF: 0.0546

Gnomad NFE AF: 0.00514

Gnomad OTH AF: 0.179

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.236 AC: 26472 AN: 112042 Hom.: 7495 Cov.: 23 AF XY: 0.216 AC XY: 7382 AN XY: 34228

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.00604

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.00258

Gnomad4 NFE AF: 0.00515

Gnomad4 OTH AF: 0.178

Alfa AF: 0.0775 Hom.: 1135

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	0.83
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332720; hg19: chrX-64815536;