14-31283458-T-G

Variant summary

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

The ENST00000551799.1(ENSG00000257831):​n.400+4324T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,914 control chromosomes in the GnomAD database, including 38,400 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 0.70 ( 38400 hom., cov: 30)

Consequence

ENSG00000257831
ENST00000551799.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.357
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=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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
ENSG00000257831ENST00000551799.1 linkn.400+4324T>G intron_variant Intron 4 of 5 3

Frequencies

GnomAD3 genomes
AF:
0.700
AC:
106277
AN:
151796
Hom.:
38356
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.835
Gnomad AMI
AF:
0.581
Gnomad AMR
AF:
0.723
Gnomad ASJ
AF:
0.607
Gnomad EAS
AF:
0.978
Gnomad SAS
AF:
0.814
Gnomad FIN
AF:
0.654
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.598
Gnomad OTH
AF:
0.695
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.700
AC:
106386
AN:
151914
Hom.:
38400
Cov.:
30
AF XY:
0.706
AC XY:
52430
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.835
Gnomad4 AMR
AF:
0.724
Gnomad4 ASJ
AF:
0.607
Gnomad4 EAS
AF:
0.978
Gnomad4 SAS
AF:
0.813
Gnomad4 FIN
AF:
0.654
Gnomad4 NFE
AF:
0.598
Gnomad4 OTH
AF:
0.697
Alfa
AF:
0.611
Hom.:
44667
Bravo
AF:
0.712
Asia WGS
AF:
0.895
AC:
3111
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
5.2
DANN
Benign
0.67

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: rs927704; hg19: chr14-31752664; API