rs7170307

Variant names:

• chr15-56445099-A-C
• rs7170307
• NM_018365.4:c.457-426T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MNS1	NM_018365.4	c.457-426T>G		intron_variant	Intron 4 of 9	ENST00000260453.4	NP_060835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MNS1	ENST00000260453.4	c.457-426T>G		intron_variant	Intron 4 of 9	1	NM_018365.4	ENSP00000260453.3
TEX9	ENST00000352903.6	c.*30-572A>C		intron_variant	Intron 12 of 12	1		ENSP00000342169.2
TEX9	ENST00000537232.5	n.*1306-572A>C		intron_variant	Intron 12 of 12	2		ENSP00000438745.2

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

African (AFR) AF: 0.246 AC: 10204 AN: 41490

American (AMR) AF: 0.456 AC: 6961 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1458 AN: 3464

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4828

European-Finnish (FIN) AF: 0.473 AC: 5001 AN: 10580

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31668 AN: 67790

Other (OTH) AF: 0.368 AC: 776 AN: 2108

Alfa AF: 0.433 Hom.: 46018

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
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7170307; hg19: chr15-56737297;