chr15-56429208-C-G

Variant names:

• chr15-56429208-C-G
• rs808730
• NM_001395496.1:c.*764C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001395496.1(TEX9):​c.*764C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEX9 NM_001395496.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

MNS1 (HGNC:29636): (meiosis specific nuclear structural 1) This gene encodes a protein highly similar to the mouse meiosis-specific nuclear structural 1 protein. The mouse protein was shown to be expressed at the pachytene stage during spermatogenesis and may function as a nuclear skeletal protein to regulate nuclear morphology during meiosis. [provided by RefSeq, Oct 2008]

MNS1 Gene-Disease associations (from GenCC):

• heterotaxy, visceral, 9, autosomal, with male infertility

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395496.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX9	NM_001395496.1	MANE Select	c.*764C>G		3_prime_UTR	Exon 12 of 12	NP_001382425.1	A0A0S2Z669
	MNS1	NM_018365.4	MANE Select	c.1396-15G>C		intron	N/A	NP_060835.1	Q8NEH6
	TEX9	NM_001385046.1		c.*764C>G		3_prime_UTR	Exon 10 of 10	NP_001371975.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX9	ENST00000696102.1	MANE Select	c.*764C>G		3_prime_UTR	Exon 12 of 12	ENSP00000512397.1	Q8N6V9-1
	MNS1	ENST00000260453.4	TSL:1 MANE Select	c.1396-15G>C		intron	N/A	ENSP00000260453.3	Q8NEH6
	TEX9	ENST00000352903.6	TSL:1	c.*29+735C>G		intron	N/A	ENSP00000342169.2	Q8N6V9-1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1385890 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 691804

African (AFR) AF: 0.00 AC: 0 AN: 30148

American (AMR) AF: 0.00 AC: 0 AN: 36898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25202

East Asian (EAS) AF: 0.00 AC: 0 AN: 37520

South Asian (SAS) AF: 0.00 AC: 0 AN: 78786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51354

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5612

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1062670

Other (OTH) AF: 0.00 AC: 0 AN: 57700

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 83102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	10
DANN	Benign	0.58
PhyloP100		0.098

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

Other links and lift over

dbSNP: rs808730; hg19: chr15-56721406;