rs12669187

Variant summary

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

The NM_032222.3(MINDY4):​c.1971+207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0714 in 152,254 control chromosomes in the GnomAD database, including 631 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 0.071 ( 631 hom., cov: 32)

Consequence

MINDY4
NM_032222.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17
Variant links:
Genes affected
MINDY4 (HGNC:21916): (MINDY lysine 48 deubiquitinase 4) Predicted to enable Lys48-specific deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MINDY4NM_032222.3 linkuse as main transcriptc.1971+207G>A intron_variant ENST00000265299.6
INMT-MINDY4NR_037598.1 linkuse as main transcriptn.2500+207G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MINDY4ENST00000265299.6 linkuse as main transcriptc.1971+207G>A intron_variant 1 NM_032222.3 P1
MINDY4ENST00000409881.1 linkuse as main transcriptn.1804+207G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0712
AC:
10833
AN:
152136
Hom.:
622
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.0219
Gnomad AMR
AF:
0.0311
Gnomad ASJ
AF:
0.0467
Gnomad EAS
AF:
0.110
Gnomad SAS
AF:
0.0931
Gnomad FIN
AF:
0.0433
Gnomad MID
AF:
0.0924
Gnomad NFE
AF:
0.0355
Gnomad OTH
AF:
0.0603
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0714
AC:
10875
AN:
152254
Hom.:
631
Cov.:
32
AF XY:
0.0719
AC XY:
5351
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.148
Gnomad4 AMR
AF:
0.0311
Gnomad4 ASJ
AF:
0.0467
Gnomad4 EAS
AF:
0.110
Gnomad4 SAS
AF:
0.0932
Gnomad4 FIN
AF:
0.0433
Gnomad4 NFE
AF:
0.0355
Gnomad4 OTH
AF:
0.0625
Alfa
AF:
0.0409
Hom.:
199
Bravo
AF:
0.0725
Asia WGS
AF:
0.107
AC:
370
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.0090
DANN
Benign
0.57

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: rs12669187; hg19: chr7-30915478; API