6-77815141-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322247.2(MEI4):​c.769-13790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 151,988 control chromosomes in the GnomAD database, including 53,051 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 0.83 (53051 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEI4	NM_001322247.2	MANE Select	c.769-13790C>T		intron	N/A	NP_001309176.1	A8MW99
	MEI4	NM_001282136.3		c.769-13790C>T		intron	N/A	NP_001269065.1	A8MW99

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEI4	ENST00000684080.1	MANE Select	c.769-13790C>T		intron	N/A	ENSP00000507827.1	A8MW99
	MEI4	ENST00000602452.3	TSL:5	c.769-13790C>T		intron	N/A	ENSP00000473370.1	A8MW99
	MEI4	ENST00000649759.1		c.769-13790C>T		intron	N/A	ENSP00000496917.1	A8MW99

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126285 AN: 151870 Hom.: 52997 Cov.: 30

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.832 AC: 126396 AN: 151988 Hom.: 53051 Cov.: 30 AF XY: 0.833 AC XY: 61852 AN XY: 74296

African (AFR) AF: 0.938 AC: 38943 AN: 41506

American (AMR) AF: 0.843 AC: 12838 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2741 AN: 3470

East Asian (EAS) AF: 0.950 AC: 4886 AN: 5144

South Asian (SAS) AF: 0.721 AC: 3472 AN: 4814

European-Finnish (FIN) AF: 0.822 AC: 8708 AN: 10588

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52266 AN: 67932

Other (OTH) AF: 0.807 AC: 1700 AN: 2106

Alfa AF: 0.816 Hom.: 8872

Bravo AF: 0.840

Asia WGS AF: 0.871 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.34
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;