19-29706248-C-T

Variant summary

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

The NM_031448.6(C19orf12):​c.160+2006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,266 control chromosomes in the GnomAD database, including 1,678 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 0.13 ( 1678 hom., cov: 33)

Consequence

C19orf12
NM_031448.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.721
Variant links:
Genes affected
C19orf12 (HGNC:25443): (chromosome 19 open reading frame 12) This gene encodes a small transmembrane protein. Mutations in this gene are a cause of neurodegeneration with brain iron accumulation-4 (NBIA4), but the specific function of the encoded protein is unknown. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

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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 = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C19orf12NM_031448.6 linkc.160+2006G>A intron_variant Intron 2 of 2 ENST00000323670.14 NP_113636.2 Q9NSK7-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C19orf12ENST00000323670.14 linkc.160+2006G>A intron_variant Intron 2 of 2 2 NM_031448.6 ENSP00000313332.9 Q9NSK7-4

Frequencies

GnomAD3 genomes
AF:
0.135
AC:
20479
AN:
152148
Hom.:
1673
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.0482
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.0893
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.233
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.108
Gnomad OTH
AF:
0.128
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.135
AC:
20506
AN:
152266
Hom.:
1678
Cov.:
33
AF XY:
0.142
AC XY:
10547
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.111
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.0893
Gnomad4 EAS
AF:
0.370
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.157
Gnomad4 NFE
AF:
0.108
Gnomad4 OTH
AF:
0.128
Alfa
AF:
0.114
Hom.:
2346
Bravo
AF:
0.137
Asia WGS
AF:
0.283
AC:
986
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
0.16
DANN
Benign
0.31

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: rs3746314; hg19: chr19-30197155; API