5-131913076-C-T

Variant names:

• chr5-131913076-C-T
• rs1355095
• NM_001303622.2:c.639-1197G>A

Variant summary

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

The NM_001303622.2(MEIKIN):​c.639-1197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,182 control chromosomes in the GnomAD database, including 56,816 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 0.86 (56816 hom., cov: 31)
• Consequence: MEIKIN NM_001303622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIKIN	NM_001303622.2	c.639-1197G>A		intron_variant	Intron 7 of 12	ENST00000442687.6	NP_001290551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEIKIN	ENST00000442687.6	c.639-1197G>A		intron_variant	Intron 7 of 12	1	NM_001303622.2	ENSP00000488568.1
ENSG00000281938	ENST00000652469.1	n.*374-1197G>A		intron_variant	Intron 25 of 25			ENSP00000498837.1

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131144 AN: 152064 Hom.: 56758 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.863 AC: 131262 AN: 152182 Hom.: 56816 Cov.: 31 AF XY: 0.862 AC XY: 64144 AN XY: 74396

African (AFR) AF: 0.932 AC: 38714 AN: 41540

American (AMR) AF: 0.882 AC: 13476 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3122 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4586 AN: 5182

South Asian (SAS) AF: 0.826 AC: 3986 AN: 4824

European-Finnish (FIN) AF: 0.815 AC: 8617 AN: 10572

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55892 AN: 67990

Other (OTH) AF: 0.861 AC: 1818 AN: 2112

Alfa AF: 0.835 Hom.: 25030

Bravo AF: 0.874

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.56
PhyloP100		0.60

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: rs1355095; hg19: chr5-131248769;