rs1398576

Variant names:

• chr6-77815141-C-G
• rs1398576
• NM_001322247.2:c.769-13790C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-77815141-C-G
• chr6-77815141-C-T

Variant summary

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

The NM_001322247.2(MEI4):​c.769-13790C>G 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: 30)
• Consequence: MEI4 NM_001322247.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 6 publications found

Genes affected

MEI4 (HGNC:43638): (meiotic double-stranded break formation protein 4) Predicted to be involved in gamete generation and meiosis I cell cycle process. Predicted to be active in lateral element. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230309 (HGNC:):

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=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322247.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEI4	NM_001322247.2	MANE Select	c.769-13790C>G		intron	N/A	NP_001309176.1
	MEI4	NM_001282136.3		c.769-13790C>G		intron	N/A	NP_001269065.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEI4	ENST00000684080.1	MANE Select	c.769-13790C>G		intron	N/A	ENSP00000507827.1
	MEI4	ENST00000602452.3	TSL:5	c.769-13790C>G		intron	N/A	ENSP00000473370.1
	MEI4	ENST00000649759.1		c.769-13790C>G		intron	N/A	ENSP00000496917.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.37
PhyloP100		-0.65

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: rs1398576; hg19: chr6-78524858;