rs667437

Variant summary

Our verdict is Benign. The variant received -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.174

Publications

5 publications found
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
MEIKINNM_001303622.2 linkc.349+2819C>T intron_variant Intron 4 of 12 ENST00000442687.6 NP_001290551.1 A0A087WXM9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MEIKINENST00000442687.6 linkc.349+2819C>T intron_variant Intron 4 of 12 1 NM_001303622.2 ENSP00000488568.1 A0A087WXM9
ENSG00000281938ENST00000652469.1 linkn.*213+4849C>T intron_variant Intron 23 of 25 ENSP00000498837.1 A0A494C116

Frequencies

GnomAD3 genomes
AF:
0.361
AC:
54773
AN:
151836
Hom.:
11769
Cov.:
32
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.:
32
AF XY:
0.361
AC XY:
26831
AN XY:
74266
show subpopulations
African (AFR)
AF:
0.608
AC:
25195
AN:
41418
American (AMR)
AF:
0.319
AC:
4877
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.346
AC:
1200
AN:
3468
East Asian (EAS)
AF:
0.497
AC:
2571
AN:
5176
South Asian (SAS)
AF:
0.269
AC:
1297
AN:
4814
European-Finnish (FIN)
AF:
0.295
AC:
3110
AN:
10526
Middle Eastern (MID)
AF:
0.282
AC:
83
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15616
AN:
67942
Other (OTH)
AF:
0.321
AC:
677
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1607
3213
4820
6426
8033
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
504
1008
1512
2016
2520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.330
Hom.:
1615
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
PhyloP100
-0.17

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

Other links and lift over

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