5-136736365-G-A

Variant summary

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

The ENST00000502421.2(ENSG00000250284):​n.79+1360G>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 0.453 in 152,084 control chromosomes in the GnomAD database, including 15,891 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 0.45 ( 15891 hom., cov: 33)

Consequence


ENST00000502421.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
Variant links:
Genes affected

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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000502421.2 linkuse as main transcriptn.79+1360G>A intron_variant, non_coding_transcript_variant 4
ENST00000656447.1 linkuse as main transcriptn.75+1360G>A intron_variant, non_coding_transcript_variant
ENST00000662288.1 linkuse as main transcriptn.176+1360G>A intron_variant, non_coding_transcript_variant
ENST00000667761.1 linkuse as main transcriptn.62+1360G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68845
AN:
151966
Hom.:
15885
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.405
Gnomad AMI
AF:
0.578
Gnomad AMR
AF:
0.445
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.690
Gnomad SAS
AF:
0.424
Gnomad FIN
AF:
0.423
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.474
Gnomad OTH
AF:
0.459
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.453
AC:
68874
AN:
152084
Hom.:
15891
Cov.:
33
AF XY:
0.451
AC XY:
33566
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.404
Gnomad4 AMR
AF:
0.444
Gnomad4 ASJ
AF:
0.405
Gnomad4 EAS
AF:
0.690
Gnomad4 SAS
AF:
0.425
Gnomad4 FIN
AF:
0.423
Gnomad4 NFE
AF:
0.474
Gnomad4 OTH
AF:
0.457
Alfa
AF:
0.389
Hom.:
2003
Bravo
AF:
0.456
Asia WGS
AF:
0.519
AC:
1803
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.27
DANN
Benign
0.27

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: rs726846; hg19: chr5-136072054; API