rs1566427

chr5-131855979-G-Achr5-131855979-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEIKIN	ENST00000442687.6	c.775-1145C>T		intron_variant		1	NM_001303622.2	P2
MEIKIN	ENST00000439905.5	c.48-4596C>T		intron_variant		3
MEIKIN	ENST00000616644.2	c.775-1145C>T		intron_variant		5		A2

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

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.790

Alfa AF: 0.779 Hom.: 5381

Bravo AF: 0.787

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.37

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;