rs7249968

Variant summary

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

The ENST00000588092.1(ENSG00000267223):​n.296-545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,700 control chromosomes in the GnomAD database, including 5,124 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 0.25 ( 5124 hom., cov: 31)

Consequence

ENSG00000267223
ENST00000588092.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.68
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=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000267223ENST00000588092.1 linkn.296-545A>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38392
AN:
151582
Hom.:
5114
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.306
Gnomad AMI
AF:
0.129
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.229
Gnomad EAS
AF:
0.160
Gnomad SAS
AF:
0.264
Gnomad FIN
AF:
0.223
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.221
Gnomad OTH
AF:
0.278
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.253
AC:
38437
AN:
151700
Hom.:
5124
Cov.:
31
AF XY:
0.255
AC XY:
18875
AN XY:
74136
show subpopulations
Gnomad4 AFR
AF:
0.306
Gnomad4 AMR
AF:
0.315
Gnomad4 ASJ
AF:
0.229
Gnomad4 EAS
AF:
0.160
Gnomad4 SAS
AF:
0.264
Gnomad4 FIN
AF:
0.223
Gnomad4 NFE
AF:
0.221
Gnomad4 OTH
AF:
0.274
Alfa
AF:
0.237
Hom.:
5500
Bravo
AF:
0.261
Asia WGS
AF:
0.226
AC:
786
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.75
DANN
Benign
0.39

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: rs7249968; hg19: chr19-30711242; API