5-1345359-A-G

Variant summary

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

The ENST00000656081.1(ENSG00000286388):​n.163A>G 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 0.487 in 152,044 control chromosomes in the GnomAD database, including 19,842 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 0.49 ( 19842 hom., cov: 33)

Consequence

ENSG00000286388
ENST00000656081.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164
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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286388ENST00000656081.1 linkn.163A>G non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
74056
AN:
151934
Hom.:
19822
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.712
Gnomad AMI
AF:
0.519
Gnomad AMR
AF:
0.351
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.182
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.450
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.434
Gnomad OTH
AF:
0.460
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.487
AC:
74120
AN:
152044
Hom.:
19842
Cov.:
33
AF XY:
0.478
AC XY:
35508
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.711
Gnomad4 AMR
AF:
0.350
Gnomad4 ASJ
AF:
0.424
Gnomad4 EAS
AF:
0.183
Gnomad4 SAS
AF:
0.212
Gnomad4 FIN
AF:
0.450
Gnomad4 NFE
AF:
0.434
Gnomad4 OTH
AF:
0.458
Alfa
AF:
0.389
Hom.:
2353
Bravo
AF:
0.494
Asia WGS
AF:
0.237
AC:
830
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.86
DANN
Benign
0.35

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: rs27996; hg19: chr5-1345474; API