rs667437
Variant names:
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
NM_001303622.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.174
Publications
5 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]
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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 |
---|---|---|---|---|---|---|---|---|
MEIKIN | NM_001303622.2 | c.349+2819C>T | intron_variant | Intron 4 of 12 | ENST00000442687.6 | NP_001290551.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MEIKIN | ENST00000442687.6 | c.349+2819C>T | intron_variant | Intron 4 of 12 | 1 | NM_001303622.2 | ENSP00000488568.1 | |||
ENSG00000281938 | ENST00000652469.1 | n.*213+4849C>T | intron_variant | Intron 23 of 25 | ENSP00000498837.1 |
Frequencies
GnomAD3 genomes AF: 0.361 AC: 54773AN: 151836Hom.: 11769 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
54773
AN:
151836
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.361 AC: 54871AN: 151954Hom.: 11809 Cov.: 32 AF XY: 0.361 AC XY: 26831AN XY: 74266 show subpopulations
GnomAD4 genome
AF:
AC:
54871
AN:
151954
Hom.:
Cov.:
32
AF XY:
AC XY:
26831
AN XY:
74266
show subpopulations
African (AFR)
AF:
AC:
25195
AN:
41418
American (AMR)
AF:
AC:
4877
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
1200
AN:
3468
East Asian (EAS)
AF:
AC:
2571
AN:
5176
South Asian (SAS)
AF:
AC:
1297
AN:
4814
European-Finnish (FIN)
AF:
AC:
3110
AN:
10526
Middle Eastern (MID)
AF:
AC:
83
AN:
294
European-Non Finnish (NFE)
AF:
AC:
15616
AN:
67942
Other (OTH)
AF:
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
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1394
AN:
3468
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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