GeneBe

rs11738335

Positions:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000505642.6(C5orf64):​n.148+10984T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 151,832 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 ( 0 hom., cov: 31)

Consequence

C5orf64
ENST00000505642.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.744
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
C5orf64NR_126523.1 linkuse as main transcriptn.140+10984T>C intron_variant
C5orf64NR_126524.1 linkuse as main transcriptn.140+10984T>C intron_variant
C5orf64NR_126525.1 linkuse as main transcriptn.66+16538T>C intron_variant
C5orf64NR_161251.1 linkuse as main transcriptn.161+10984T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
C5orf64ENST00000505642.6 linkuse as main transcriptn.148+10984T>C intron_variant 2
C5orf64ENST00000507461.2 linkuse as main transcriptn.139+16538T>C intron_variant 4
C5orf64ENST00000510414.4 linkuse as main transcriptn.161+10984T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
151832
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000969
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
151832
Hom.:
0
Cov.:
31
AF XY:
0.0000270
AC XY:
2
AN XY:
74122
show subpopulations
Gnomad4 AFR
AF:
0.0000969
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.40
DANN
Benign
0.53

Splicing

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: rs11738335; hg19: chr5-60950211; API