rs10863899

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000417794.1(ENSG00000223649):​n.450A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,118 control chromosomes in the GnomAD database, including 17,490 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17484 hom., cov: 33)
Exomes 𝑓: 0.36 ( 6 hom. )

Consequence

ENSG00000223649
ENST00000417794.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.463
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 1-211492876-A-G is Benign according to our data. Variant chr1-211492876-A-G is described in ClinVar as [Benign]. Clinvar id is 295305.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000223649ENST00000417794.1 linkn.450A>G non_coding_transcript_exon_variant 2/23

Frequencies

GnomAD3 genomes
AF:
0.466
AC:
70871
AN:
151944
Hom.:
17461
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.624
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.374
Gnomad ASJ
AF:
0.448
Gnomad EAS
AF:
0.424
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.325
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.460
GnomAD4 exome
AF:
0.357
AC:
20
AN:
56
Hom.:
6
Cov.:
0
AF XY:
0.438
AC XY:
14
AN XY:
32
show subpopulations
Gnomad4 AFR exome
AF:
0.750
Gnomad4 FIN exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.262
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.467
AC:
70953
AN:
152062
Hom.:
17484
Cov.:
33
AF XY:
0.457
AC XY:
34010
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.624
Gnomad4 AMR
AF:
0.374
Gnomad4 ASJ
AF:
0.448
Gnomad4 EAS
AF:
0.424
Gnomad4 SAS
AF:
0.398
Gnomad4 FIN
AF:
0.325
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.461
Alfa
AF:
0.428
Hom.:
28842
Bravo
AF:
0.475
Asia WGS
AF:
0.452
AC:
1575
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Leber congenital amaurosis 12 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.89
DANN
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10863899; hg19: chr1-211666218; API