rs667437

Positions:

• chr5-131939816-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001303622.2(MEIKIN):​c.349+2819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,954 control chromosomes in the GnomAD database, including 11,809 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 0.36 (11809 hom., cov: 32)
• Consequence: MEIKIN NM_001303622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEIKIN	NM_001303622.2	c.349+2819C>T		intron_variant		ENST00000442687.6	NP_001290551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEIKIN	ENST00000442687.6	c.349+2819C>T		intron_variant		1	NM_001303622.2	ENSP00000488568.1
ENSG00000281938	ENST00000652469.1	n.*213+4849C>T		intron_variant				ENSP00000498837.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54773 AN: 151836 Hom.: 11769 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.361 AC: 54871 AN: 151954 Hom.: 11809 Cov.: 32 AF XY: 0.361 AC XY: 26831 AN XY: 74266

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.321

Alfa AF: 0.321 Hom.: 1468

Bravo AF: 0.377

Asia WGS AF: 0.402 AC: 1394 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.62

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: rs667437; hg19: chr5-131275509; COSMIC: COSV68856625; COSMIC: COSV68856625;