rs1543245

Variant summary

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

The ENST00000561208.6(MEIS2):​c.754+18462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,070 control chromosomes in the GnomAD database, including 3,857 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 0.22 ( 3857 hom., cov: 33)

Consequence

MEIS2
ENST00000561208.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.948
Variant links:
Genes affected
MEIS2 (HGNC:7001): (Meis homeobox 2) This gene encodes a homeobox protein belonging to the TALE ('three amino acid loop extension') family of homeodomain-containing proteins. TALE homeobox proteins are highly conserved transcription regulators, and several members have been shown to be essential contributors to developmental programs. Multiple transcript variants encoding distinct isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MEIS2NM_170675.5 linkuse as main transcriptc.754+18462T>C intron_variant ENST00000561208.6 NP_733775.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MEIS2ENST00000561208.6 linkuse as main transcriptc.754+18462T>C intron_variant 1 NM_170675.5 ENSP00000453793 O14770-1

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33866
AN:
151952
Hom.:
3858
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.0833
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.192
Gnomad EAS
AF:
0.319
Gnomad SAS
AF:
0.248
Gnomad FIN
AF:
0.212
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.233
Gnomad OTH
AF:
0.211
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.223
AC:
33875
AN:
152070
Hom.:
3857
Cov.:
33
AF XY:
0.224
AC XY:
16669
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.212
Gnomad4 AMR
AF:
0.191
Gnomad4 ASJ
AF:
0.192
Gnomad4 EAS
AF:
0.318
Gnomad4 SAS
AF:
0.248
Gnomad4 FIN
AF:
0.212
Gnomad4 NFE
AF:
0.233
Gnomad4 OTH
AF:
0.211
Alfa
AF:
0.232
Hom.:
8354
Bravo
AF:
0.220
Asia WGS
AF:
0.253
AC:
879
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.4
DANN
Benign
0.55

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.

Other links and lift over

dbSNP: rs1543245; hg19: chr15-37357510; API