Variant rs667437 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.174

Variant links:

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]

MEIKIN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	UniProt
MEIKIN	NM_001303622.2 linkuse as main transcript	c.349+2819C>T		intron_variant		ENST00000442687.6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MEIKIN	ENST00000442687.6 linkuse as main transcript	c.349+2819C>T	intron_variant	1	NM_001303622.2	P2
MEIKIN	ENST00000616644.2 linkuse as main transcript	c.349+2819C>T	intron_variant	5		A2
MEIKIN	ENST00000425320.1 linkuse as main transcript	n.189+2819C>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54773

AN:

151836

Hom.:

11769

Cov.:

show subpopulations

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.:

AF XY:

0.361

AC XY:

26831

AN XY:

74266

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over