rs1434939

Variant summary

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

The NM_052958.4(C8orf34):​c.1106-48349T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,016 control chromosomes in the GnomAD database, including 8,609 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 0.33 ( 8609 hom., cov: 32)

Consequence

C8orf34
NM_052958.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450
Variant links:
Genes affected
C8orf34 (HGNC:30905): (chromosome 8 open reading frame 34) This gene encodes a protein that is related to the cyclic AMP dependent protein kinase regulators. Naturally occurring mutations in this gene are associated with an increased risk for severe toxicities, such as diarrhea and neutropenia, in patients undergoing chemotherapeutic treatment. [provided by RefSeq, Mar 2017]

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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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C8orf34NM_052958.4 linkuse as main transcriptc.1106-48349T>A intron_variant ENST00000518698.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C8orf34ENST00000518698.6 linkuse as main transcriptc.1106-48349T>A intron_variant 2 NM_052958.4 P2Q49A92-6
C8orf34ENST00000337103.8 linkuse as main transcriptc.773-48349T>A intron_variant 1 Q49A92-2
C8orf34ENST00000521406.5 linkuse as main transcriptc.*239-48349T>A intron_variant, NMD_transcript_variant 2
C8orf34ENST00000518515.1 linkuse as main transcriptn.130+58878T>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.330
AC:
50156
AN:
151898
Hom.:
8604
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.230
Gnomad AMI
AF:
0.381
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.379
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.374
Gnomad MID
AF:
0.316
Gnomad NFE
AF:
0.380
Gnomad OTH
AF:
0.361
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.330
AC:
50182
AN:
152016
Hom.:
8609
Cov.:
32
AF XY:
0.331
AC XY:
24584
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.230
Gnomad4 AMR
AF:
0.353
Gnomad4 ASJ
AF:
0.379
Gnomad4 EAS
AF:
0.288
Gnomad4 SAS
AF:
0.307
Gnomad4 FIN
AF:
0.374
Gnomad4 NFE
AF:
0.380
Gnomad4 OTH
AF:
0.358
Alfa
AF:
0.348
Hom.:
1169
Bravo
AF:
0.328
Asia WGS
AF:
0.249
AC:
865
AN:
3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.30

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: rs1434939; hg19: chr8-69504262; API