rs363691

Variant names:

• chr2-74614442-C-A
• rs363691
• NM_001321739.2:c.426+522G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-74614442-C-A
• chr2-74614442-C-G
• chr2-74614442-C-T

Variant summary

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

The NM_001321739.2(M1AP):​c.426+522G>T variant causes a intron 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: 32)
• Consequence: M1AP NM_001321739.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 7 publications found

Genes affected

M1AP (HGNC:25183): (meiosis 1 associated protein) This gene encodes a protein that is likely to function in progression of meiosis. A similar protein in mouse plays a role in gametogenesis in both sexes. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

M1AP Gene-Disease associations (from GenCC):

• spermatogenic failure 48

  Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

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=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321739.2. 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
	M1AP	NM_001321739.2	MANE Select	c.426+522G>T		intron	N/A	NP_001308668.1	Q8TC57-1
	M1AP	NM_138804.5		c.426+522G>T		intron	N/A	NP_620159.2
	M1AP	NM_001281296.2		c.426+522G>T		intron	N/A	NP_001268225.1	Q8TC57-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	M1AP	ENST00000421985.2	TSL:2 MANE Select	c.426+522G>T		intron	N/A	ENSP00000414882.2	Q8TC57-1
	M1AP	ENST00000290536.9	TSL:1	c.426+522G>T		intron	N/A	ENSP00000290536.5	Q8TC57-1
	M1AP	ENST00000409585.5	TSL:5	c.426+522G>T		intron	N/A	ENSP00000386793.1	Q8TC57-4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.064

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: rs363691; hg19: chr2-74841569;