dbSNP rs16935110: C8orf34:c.*238A>T (chr8-68818484-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_052958.4(C8orf34):c.*238A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 470,834 control chromosomes in the GnomAD database, including 7,039 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 0.15 ( 1858 hom., cov: 32)

Exomes 𝑓: 0.16 ( 5181 hom. )

Consequence

C8orf34
NM_052958.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.561

Publications

7 publications found

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]

C8orf34 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052958.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
C8orf34	NM_052958.4	MANE Select	c.*238A>T	3_prime_UTR	Exon 14 of 14	NP_443190.2
C8orf34	NM_001349476.1		c.*238A>T	3_prime_UTR	Exon 14 of 14	NP_001336405.1
C8orf34	NM_001349477.1		c.*238A>T	3_prime_UTR	Exon 13 of 13	NP_001336406.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
C8orf34	ENST00000518698.6	TSL:2 MANE Select	c.*238A>T	3_prime_UTR	Exon 14 of 14	ENSP00000427820.1
C8orf34	ENST00000337103.8	TSL:1	c.*238A>T	3_prime_UTR	Exon 13 of 13	ENSP00000337174.4
C8orf34	ENST00000924297.1		c.*238A>T	3_prime_UTR	Exon 15 of 15	ENSP00000594356.1

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22327

AN:

151940

Hom.:

1859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.141

GnomAD4 exome

AF:

0.159

AC:

50549

AN:

318778

Hom.:

5181

Cov.:

AF XY:

0.160

AC XY:

26276

AN XY:

164328

show subpopulations

African (AFR)

AF:

0.106

AC:

1064

AN:

10026

American (AMR)

AF:

0.116

AC:

1441

AN:

12422

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

1499

AN:

10418

East Asian (EAS)

AF:

0.428

AC:

11262

AN:

26286

South Asian (SAS)

AF:

0.221

AC:

3273

AN:

14840

European-Finnish (FIN)

AF:

0.155

AC:

4778

AN:

30882

Middle Eastern (MID)

AF:

0.120

AC:

173

AN:

1440

European-Non Finnish (NFE)

AF:

0.125

AC:

24184

AN:

193182

Other (OTH)

AF:

0.149

AC:

2875

AN:

19282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

1653

3307

4960

6614

8267

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

220

440

660

880

1100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.147

AC:

22332

AN:

152056

Hom.:

1858

Cov.:

AF XY:

0.152

AC XY:

11295

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.124

AC:

5160

AN:

41496

American (AMR)

AF:

0.124

AC:

1889

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

572

AN:

3468

East Asian (EAS)

AF:

0.428

AC:

2203

AN:

5152

South Asian (SAS)

AF:

0.271

AC:

1304

AN:

4820

European-Finnish (FIN)

AF:

0.163

AC:

1727

AN:

10582

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9020

AN:

67972

Other (OTH)

AF:

0.140

AC:

294

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

967

1934

2900

3867

4834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.142

Hom.:

203

Bravo

AF:

0.139

Asia WGS

AF:

0.333

AC:

1154

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.2

(source)

DANN

Benign

0.69

PhyloP100

0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over