rs6060269

Variant summary

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

The NM_001355008.2(MMP24-AS1-EDEM2):​c.-16-1777G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.17 ( 385 hom., cov: 0)

Consequence

MMP24-AS1-EDEM2
NM_001355008.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.866
Variant links:
Genes affected

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=-0.99).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MMP24-AS1-EDEM2NM_001355008.2 linkuse as main transcriptc.-16-1777G>T intron_variant NP_001341937.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.169
AC:
3295
AN:
19448
Hom.:
380
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0881
Gnomad AMI
AF:
0.0984
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.149
Gnomad SAS
AF:
0.226
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.281
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.205
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.170
AC:
3319
AN:
19494
Hom.:
385
Cov.:
0
AF XY:
0.188
AC XY:
1770
AN XY:
9408
show subpopulations
Gnomad4 AFR
AF:
0.0897
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.151
Gnomad4 EAS
AF:
0.151
Gnomad4 SAS
AF:
0.226
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.10
DANN
Benign
0.64

Splicing

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: rs6060269; hg19: chr20-33736515; API