chr14-65268966-T-C

Variant summary

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

The ENST00000484315.1(RPL36AP2):​n.138T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 223,070 control chromosomes in the GnomAD database, including 7,183 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 0.23 ( 6302 hom., cov: 32)
Exomes 𝑓: 0.14 ( 881 hom. )

Consequence

RPL36AP2
ENST00000484315.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.21
Variant links:
Genes affected
RPL36AP2 (HGNC:19777): (ribosomal protein L36a pseudogene 2)

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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL36AP2ENST00000484315.1 linkuse as main transcriptn.138T>C non_coding_transcript_exon_variant 1/1
ENST00000555736.1 linkuse as main transcriptn.153-21243A>G intron_variant, non_coding_transcript_variant 5
ENST00000553754.1 linkuse as main transcriptn.368+479A>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.227
AC:
34552
AN:
151992
Hom.:
6276
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.499
Gnomad AMI
AF:
0.142
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.280
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.0907
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.231
GnomAD4 exome
AF:
0.139
AC:
9841
AN:
70960
Hom.:
881
Cov.:
0
AF XY:
0.137
AC XY:
5816
AN XY:
42440
show subpopulations
Gnomad4 AFR exome
AF:
0.530
Gnomad4 AMR exome
AF:
0.102
Gnomad4 ASJ exome
AF:
0.136
Gnomad4 EAS exome
AF:
0.288
Gnomad4 SAS exome
AF:
0.134
Gnomad4 FIN exome
AF:
0.110
Gnomad4 NFE exome
AF:
0.118
Gnomad4 OTH exome
AF:
0.118
GnomAD4 genome
AF:
0.228
AC:
34622
AN:
152110
Hom.:
6302
Cov.:
32
AF XY:
0.224
AC XY:
16673
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.499
Gnomad4 AMR
AF:
0.166
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.280
Gnomad4 SAS
AF:
0.120
Gnomad4 FIN
AF:
0.0907
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.136
Hom.:
1107
Bravo
AF:
0.246
Asia WGS
AF:
0.238
AC:
828
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
5.6
DANN
Benign
0.56

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: rs1256517; hg19: chr14-65735684; COSMIC: COSV72078052; API