rs7170307

Positions:

• chr15-56445099-A-C
• chr15-56445099-A-T

Variant summary

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

The NM_018365.4(MNS1):​c.457-426T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,896 control chromosomes in the GnomAD database, including 12,641 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 0.39 (12641 hom., cov: 32)
• Consequence: MNS1 NM_018365.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

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]

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MNS1	NM_018365.4	c.457-426T>G		intron_variant		ENST00000260453.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MNS1	ENST00000260453.4	c.457-426T>G		intron_variant		1	NM_018365.4	P1
TEX9	ENST00000352903.6	c.*30-572A>C		intron_variant		1		P1
TEX9	ENST00000537232.5	c.*1306-572A>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59929 AN: 151778 Hom.: 12640 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.395 AC: 59954 AN: 151896 Hom.: 12641 Cov.: 32 AF XY: 0.395 AC XY: 29325 AN XY: 74232

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.368

Alfa AF: 0.442 Hom.: 29780

Bravo AF: 0.388

Asia WGS AF: 0.331 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7170307; hg19: chr15-56737297;