rs7248162

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,826 control chromosomes in the GnomAD database, including 21,340 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 0.52 ( 21340 hom., cov: 31)

Consequence

ENSG00000267114
ENST00000591646.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.542
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 (AFR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000267114ENST00000591646.1 linkn.114-403A>G intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.522
AC:
79241
AN:
151706
Hom.:
21305
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.619
Gnomad AMI
AF:
0.431
Gnomad AMR
AF:
0.576
Gnomad ASJ
AF:
0.453
Gnomad EAS
AF:
0.553
Gnomad SAS
AF:
0.586
Gnomad FIN
AF:
0.489
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.456
Gnomad OTH
AF:
0.501
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.522
AC:
79324
AN:
151826
Hom.:
21340
Cov.:
31
AF XY:
0.525
AC XY:
38935
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.620
Gnomad4 AMR
AF:
0.576
Gnomad4 ASJ
AF:
0.453
Gnomad4 EAS
AF:
0.553
Gnomad4 SAS
AF:
0.584
Gnomad4 FIN
AF:
0.489
Gnomad4 NFE
AF:
0.456
Gnomad4 OTH
AF:
0.502
Alfa
AF:
0.508
Hom.:
2611
Bravo
AF:
0.534
Asia WGS
AF:
0.580
AC:
2016
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
9.3
DANN
Benign
0.58

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: rs7248162; hg19: chr19-45454686; API