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GeneBe

rs17223072

Positions:

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.401+5029A>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 0.0912 in 152,160 control chromosomes in the GnomAD database, including 689 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 0.091 ( 689 hom., cov: 31)

Consequence


ENST00000552856.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105369844XR_007063375.1 linkuse as main transcriptn.1371+5029A>G intron_variant, non_coding_transcript_variant
LOC105369844XR_007063374.1 linkuse as main transcriptn.691+5029A>G intron_variant, non_coding_transcript_variant
LOC105369844XR_007063376.1 linkuse as main transcriptn.2298+5029A>G intron_variant, non_coding_transcript_variant
LOC105369844XR_007063377.1 linkuse as main transcriptn.2298+5029A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000552856.1 linkuse as main transcriptn.401+5029A>G intron_variant, non_coding_transcript_variant 3
ENST00000651075.1 linkuse as main transcriptn.323-1652T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0912
AC:
13864
AN:
152042
Hom.:
688
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0369
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.111
Gnomad ASJ
AF:
0.0974
Gnomad EAS
AF:
0.0830
Gnomad SAS
AF:
0.0822
Gnomad FIN
AF:
0.114
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.116
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0912
AC:
13872
AN:
152160
Hom.:
689
Cov.:
31
AF XY:
0.0914
AC XY:
6797
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0367
Gnomad4 AMR
AF:
0.111
Gnomad4 ASJ
AF:
0.0974
Gnomad4 EAS
AF:
0.0836
Gnomad4 SAS
AF:
0.0831
Gnomad4 FIN
AF:
0.114
Gnomad4 NFE
AF:
0.116
Gnomad4 OTH
AF:
0.109
Alfa
AF:
0.106
Hom.:
171
Bravo
AF:
0.0883
Asia WGS
AF:
0.0650
AC:
225
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
1.2
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: rs17223072; hg19: chr12-76080856; API