5-131855979-G-C

Position:

• chr5-131855979-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001303622.2(MEIKIN):​c.775-1145C>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: 31)
• Consequence: MEIKIN NM_001303622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

Genes affected

MEIKIN (HGNC:51253): (meiotic kinetochore factor) Predicted to be involved in meiotic chromosome segregation. Predicted to be located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000281938 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEIKIN	NM_001303622.2	c.775-1145C>G		intron_variant		ENST00000442687.6	NP_001290551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEIKIN	ENST00000442687.6	c.775-1145C>G		intron_variant		1	NM_001303622.2	ENSP00000488568.1
MEIKIN	ENST00000616644.2	c.775-1145C>G		intron_variant		5		ENSP00000481155.1
MEIKIN	ENST00000439905.5	c.46-4596C>G		intron_variant		3		ENSP00000488457.1
ENSG00000281938	ENST00000413683.5	n.*629-1145C>G		intron_variant		2		ENSP00000415140.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566427; hg19: chr5-131191672;