NM_001303622.2:c.775-1145C>T

Variant names:

• chr5-131855979-G-A
• rs1566427
• NM_001303622.2:c.775-1145C>T

Variant summary

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

The NM_001303622.2(MEIKIN):​c.775-1145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,160 control chromosomes in the GnomAD database, including 46,991 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 0.78 (46991 hom., cov: 31)
• Consequence: MEIKIN NM_001303622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303622.2. 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
	MEIKIN	NM_001303622.2	MANE Select	c.775-1145C>T		intron	N/A	NP_001290551.1	A0A087WXM9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEIKIN	ENST00000442687.6	TSL:1 MANE Select	c.775-1145C>T		intron	N/A	ENSP00000488568.1	A0A087WXM9
	MEIKIN	ENST00000616644.2	TSL:5	c.775-1145C>T		intron	N/A	ENSP00000481155.1	A0A0G2JND4
	MEIKIN	ENST00000439905.5	TSL:3	c.46-4596C>T		intron	N/A	ENSP00000488457.1	A0A0J9YXL7

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119180 AN: 152042 Hom.: 46957 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.784 AC: 119267 AN: 152160 Hom.: 46991 Cov.: 31 AF XY: 0.778 AC XY: 57862 AN XY: 74374

African (AFR) AF: 0.828 AC: 34364 AN: 41508

American (AMR) AF: 0.751 AC: 11486 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2500 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2620 AN: 5158

South Asian (SAS) AF: 0.743 AC: 3585 AN: 4822

European-Finnish (FIN) AF: 0.715 AC: 7563 AN: 10582

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54573 AN: 68014

Other (OTH) AF: 0.790 AC: 1666 AN: 2110

Alfa AF: 0.780 Hom.: 5637

Bravo AF: 0.787

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-0.70

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: rs1566427; hg19: chr5-131191672;