Menu
GeneBe

rs17367118

Variant summary

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

The ENST00000657880.1(null):n.1125-907G>A 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 0.15 in 152,054 control chromosomes in the GnomAD database, including 2,226 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 0.15 ( 2226 hom., cov: 32)

Consequence


ENST00000657880.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.695
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105373595XR_923292.3 linkuse as main transcriptn.1308-907G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000657880.1 linkuse as main transcriptn.1125-907G>A intron_variant, non_coding_transcript_variant
ENST00000655733.1 linkuse as main transcriptn.2979-907G>A intron_variant, non_coding_transcript_variant
ENST00000687364.1 linkuse as main transcriptn.435-907G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.150
AC:
22773
AN:
151936
Hom.:
2226
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0398
Gnomad AMI
AF:
0.124
Gnomad AMR
AF:
0.123
Gnomad ASJ
AF:
0.0810
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.0828
Gnomad FIN
AF:
0.213
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.133
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.150
AC:
22776
AN:
152054
Hom.:
2226
Cov.:
32
AF XY:
0.146
AC XY:
10859
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.0396
Gnomad4 AMR
AF:
0.123
Gnomad4 ASJ
AF:
0.0810
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.0827
Gnomad4 FIN
AF:
0.213
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.203
Hom.:
3980
Bravo
AF:
0.138
Asia WGS
AF:
0.112
AC:
389
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.49
Dann
Benign
0.45

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: rs17367118; hg19: chr2-123641611; API