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GeneBe

rs13179413

Variant summary

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

The NR_161255.1(C5orf67):n.236-16083G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,052 control chromosomes in the GnomAD database, including 5,112 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 0.25 ( 5112 hom., cov: 32)

Consequence

C5orf67
NR_161255.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281
Variant links:
Genes affected
C5orf67 (HGNC:51252): (chromosome 5 putative open reading frame 67)

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=-0.67).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
C5orf67NR_161255.1 linkuse as main transcriptn.236-16083G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
C5orf67ENST00000648716.1 linkuse as main transcriptn.212-16083G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.255
AC:
38681
AN:
151934
Hom.:
5108
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.322
Gnomad EAS
AF:
0.133
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.266
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.279
Gnomad OTH
AF:
0.257
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.255
AC:
38700
AN:
152052
Hom.:
5112
Cov.:
32
AF XY:
0.252
AC XY:
18745
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.227
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.322
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.229
Gnomad4 FIN
AF:
0.266
Gnomad4 NFE
AF:
0.279
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.271
Hom.:
4202
Bravo
AF:
0.252
Asia WGS
AF:
0.212
AC:
737
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
1.9
Dann
Benign
0.91

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: rs13179413; hg19: chr5-55868097; COSMIC: COSV71246419; API