rs4129540

Variant summary

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

The NR_161255.1(C5orf67):​n.235+22991G>C 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 0.778 in 152,204 control chromosomes in the GnomAD database, including 46,638 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 0.78 ( 46638 hom., cov: 33)

Consequence

C5orf67
NR_161255.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.563
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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
C5orf67NR_161255.1 linkuse as main transcriptn.235+22991G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
C5orf67ENST00000648716.1 linkuse as main transcriptn.211+22991G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.778
AC:
118382
AN:
152086
Hom.:
46602
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.542
Gnomad AMR
AF:
0.793
Gnomad ASJ
AF:
0.762
Gnomad EAS
AF:
0.672
Gnomad SAS
AF:
0.852
Gnomad FIN
AF:
0.745
Gnomad MID
AF:
0.835
Gnomad NFE
AF:
0.716
Gnomad OTH
AF:
0.791
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.778
AC:
118471
AN:
152204
Hom.:
46638
Cov.:
33
AF XY:
0.779
AC XY:
57990
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.895
Gnomad4 AMR
AF:
0.793
Gnomad4 ASJ
AF:
0.762
Gnomad4 EAS
AF:
0.671
Gnomad4 SAS
AF:
0.850
Gnomad4 FIN
AF:
0.745
Gnomad4 NFE
AF:
0.716
Gnomad4 OTH
AF:
0.791
Alfa
AF:
0.739
Hom.:
4933
Bravo
AF:
0.783
Asia WGS
AF:
0.800
AC:
2782
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.27
DANN
Benign
0.35

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: rs4129540; hg19: chr5-55878858; API