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GeneBe

rs17066842

Positions:

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000658928.1(ENSG00000285681):​n.156+44046G>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 0.0757 in 152,052 control chromosomes in the GnomAD database, including 752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.076 ( 752 hom., cov: 32)

Consequence


ENST00000658928.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.943
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.89).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 18-60373391-G-A is Benign according to our data. Variant chr18-60373391-G-A is described in Lovd as [Likely_benign].
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000658928.1 linkuse as main transcriptn.156+44046G>A intron_variant, non_coding_transcript_variant
ENST00000650201.1 linkuse as main transcriptn.113+44046G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0757
AC:
11497
AN:
151940
Hom.:
748
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.0581
Gnomad AMR
AF:
0.0369
Gnomad ASJ
AF:
0.0240
Gnomad EAS
AF:
0.0201
Gnomad SAS
AF:
0.0349
Gnomad FIN
AF:
0.0245
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0379
Gnomad OTH
AF:
0.0669
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:
0.0757
AC:
11512
AN:
152052
Hom.:
752
Cov.:
32
AF XY:
0.0743
AC XY:
5527
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.182
Gnomad4 AMR
AF:
0.0368
Gnomad4 ASJ
AF:
0.0240
Gnomad4 EAS
AF:
0.0199
Gnomad4 SAS
AF:
0.0339
Gnomad4 FIN
AF:
0.0245
Gnomad4 NFE
AF:
0.0379
Gnomad4 OTH
AF:
0.0662
Alfa
AF:
0.0780
Hom.:
123
Bravo
AF:
0.0817
Asia WGS
AF:
0.0270
AC:
93
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.8
DANN
Benign
0.34

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: rs17066842; hg19: chr18-58040624; API