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rs10042486

chr5-63965502-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000502882.1(ENSG00000248285):n.97-7487G>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 0.576 in 151,620 control chromosomes in the GnomAD database, including 26,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.58 ( 26145 hom., cov: 31)

Consequence


ENST00000502882.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.484
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-63965502-C-T is Benign according to our data. Variant chr5-63965502-C-T is described in ClinVar as [Benign]. Clinvar id is 1252728.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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
ENST00000502882.1 linkuse as main transcriptn.97-7487G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.576
AC:
87204
AN:
151504
Hom.:
26104
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.727
Gnomad AMI
AF:
0.700
Gnomad AMR
AF:
0.520
Gnomad ASJ
AF:
0.535
Gnomad EAS
AF:
0.792
Gnomad SAS
AF:
0.591
Gnomad FIN
AF:
0.428
Gnomad MID
AF:
0.661
Gnomad NFE
AF:
0.501
Gnomad OTH
AF:
0.571
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:
0.576
AC:
87291
AN:
151620
Hom.:
26145
Cov.:
31
AF XY:
0.573
AC XY:
42469
AN XY:
74086
show subpopulations
Gnomad4 AFR
AF:
0.728
Gnomad4 AMR
AF:
0.520
Gnomad4 ASJ
AF:
0.535
Gnomad4 EAS
AF:
0.792
Gnomad4 SAS
AF:
0.589
Gnomad4 FIN
AF:
0.428
Gnomad4 NFE
AF:
0.501
Gnomad4 OTH
AF:
0.572
Alfa
AF:
0.517
Hom.:
21554
Bravo
AF:
0.589
Asia WGS
AF:
0.667
AC:
2318
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMar 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
1.4
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: rs10042486; hg19: chr5-63261329; API