5-69030471-T-C

Variant summary

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

The ENST00000696797.1(ENSG00000249335):​n.466+8048A>G 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 0.298 in 152,110 control chromosomes in the GnomAD database, including 8,645 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 0.30 ( 8645 hom., cov: 32)

Consequence


ENST00000696797.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323
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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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
ENST00000696797.1 linkuse as main transcriptn.466+8048A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.299
AC:
45378
AN:
151992
Hom.:
8647
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0794
Gnomad AMI
AF:
0.190
Gnomad AMR
AF:
0.434
Gnomad ASJ
AF:
0.493
Gnomad EAS
AF:
0.131
Gnomad SAS
AF:
0.192
Gnomad FIN
AF:
0.330
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.407
Gnomad OTH
AF:
0.331
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.298
AC:
45374
AN:
152110
Hom.:
8645
Cov.:
32
AF XY:
0.294
AC XY:
21844
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.0792
Gnomad4 AMR
AF:
0.434
Gnomad4 ASJ
AF:
0.493
Gnomad4 EAS
AF:
0.131
Gnomad4 SAS
AF:
0.192
Gnomad4 FIN
AF:
0.330
Gnomad4 NFE
AF:
0.407
Gnomad4 OTH
AF:
0.327
Alfa
AF:
0.338
Hom.:
1231
Bravo
AF:
0.301
Asia WGS
AF:
0.182
AC:
629
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
10
DANN
Benign
0.74

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: rs3923114; hg19: chr5-68326298; API