rs1161397

Variant summary

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

The ENST00000454135.1(ENSG00000230472):​n.179+8022C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 150,924 control chromosomes in the GnomAD database, including 5,068 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 0.21 ( 5068 hom., cov: 31)

Consequence

ENSG00000230472
ENST00000454135.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.598
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=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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
ENSG00000230472ENST00000431394.5 linkn.104+8022C>T intron_variant Intron 1 of 4 3
ENSG00000230472ENST00000454135.1 linkn.179+8022C>T intron_variant Intron 2 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.208
AC:
31420
AN:
150806
Hom.:
5046
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.458
Gnomad AMI
AF:
0.143
Gnomad AMR
AF:
0.134
Gnomad ASJ
AF:
0.180
Gnomad EAS
AF:
0.00747
Gnomad SAS
AF:
0.125
Gnomad FIN
AF:
0.0991
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.114
Gnomad OTH
AF:
0.187
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.209
AC:
31481
AN:
150924
Hom.:
5068
Cov.:
31
AF XY:
0.204
AC XY:
15068
AN XY:
73702
show subpopulations
Gnomad4 AFR
AF:
0.458
Gnomad4 AMR
AF:
0.134
Gnomad4 ASJ
AF:
0.180
Gnomad4 EAS
AF:
0.00748
Gnomad4 SAS
AF:
0.125
Gnomad4 FIN
AF:
0.0991
Gnomad4 NFE
AF:
0.114
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.122
Hom.:
2381
Bravo
AF:
0.221
Asia WGS
AF:
0.0860
AC:
299
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.65
DANN
Benign
0.19

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: rs1161397; hg19: chr6-50596453; API