rs1268722

Variant summary

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

The NM_018245.3(OGDHL):​c.1862-186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,248 control chromosomes in the GnomAD database, including 13,542 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 0.38 ( 13542 hom., cov: 35)

Consequence

OGDHL
NM_018245.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.875
Variant links:
Genes affected
OGDHL (HGNC:25590): (oxoglutarate dehydrogenase L) The protein encoded by this gene is similar to oxoglutarate dehydrogenase (OGDH) of the OGDH complex, which degrades glucose and glutamate. This gene encodes several isoforms, including some that appear to localize to mitochondria. The encoded protein down-regulates the AKT signaling cascade and can suppress the growth of cervical cancer cells. [provided by RefSeq, Dec 2016]

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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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OGDHLNM_018245.3 linkuse as main transcriptc.1862-186C>T intron_variant ENST00000374103.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OGDHLENST00000374103.9 linkuse as main transcriptc.1862-186C>T intron_variant 1 NM_018245.3 P1Q9ULD0-1
OGDHLENST00000419399.4 linkuse as main transcriptc.1691-186C>T intron_variant 2 Q9ULD0-2
OGDHLENST00000432695.2 linkuse as main transcriptc.1235-186C>T intron_variant 2 Q9ULD0-3

Frequencies

GnomAD3 genomes
AF:
0.378
AC:
57577
AN:
152132
Hom.:
13543
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.111
Gnomad AMI
AF:
0.487
Gnomad AMR
AF:
0.471
Gnomad ASJ
AF:
0.331
Gnomad EAS
AF:
0.871
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.503
Gnomad MID
AF:
0.357
Gnomad NFE
AF:
0.462
Gnomad OTH
AF:
0.396
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.378
AC:
57580
AN:
152248
Hom.:
13542
Cov.:
35
AF XY:
0.383
AC XY:
28472
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.111
Gnomad4 AMR
AF:
0.470
Gnomad4 ASJ
AF:
0.331
Gnomad4 EAS
AF:
0.871
Gnomad4 SAS
AF:
0.411
Gnomad4 FIN
AF:
0.503
Gnomad4 NFE
AF:
0.462
Gnomad4 OTH
AF:
0.400
Alfa
AF:
0.428
Hom.:
6531
Bravo
AF:
0.370
Asia WGS
AF:
0.617
AC:
2145
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.0
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1268722; hg19: chr10-50951210; API