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GeneBe

12-53893661-C-G

Variant summary

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

The ENST00000663306.1(ENSG00000286069):n.574-2536C>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 0.382 in 151,910 control chromosomes in the GnomAD database, including 11,376 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 0.38 ( 11376 hom., cov: 31)

Consequence


ENST00000663306.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.760
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=-0.91).
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 = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107984525XR_002957415.2 linkuse as main transcriptn.452-2536C>G intron_variant, non_coding_transcript_variant
LOC107984525XR_001749153.2 linkuse as main transcriptn.376-2536C>G intron_variant, non_coding_transcript_variant
LOC107984525XR_007063319.1 linkuse as main transcriptn.1495-2536C>G intron_variant, non_coding_transcript_variant
LOC107984525XR_007063320.1 linkuse as main transcriptn.323-2536C>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000663306.1 linkuse as main transcriptn.574-2536C>G intron_variant, non_coding_transcript_variant
ENST00000652339.1 linkuse as main transcriptn.510-2536C>G intron_variant, non_coding_transcript_variant
ENST00000654713.1 linkuse as main transcriptn.318-2536C>G intron_variant, non_coding_transcript_variant
ENST00000656247.1 linkuse as main transcriptn.345-2536C>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.383
AC:
58076
AN:
151790
Hom.:
11370
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.415
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.278
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.228
Gnomad SAS
AF:
0.363
Gnomad FIN
AF:
0.320
Gnomad MID
AF:
0.318
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.354
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:
0.382
AC:
58095
AN:
151910
Hom.:
11376
Cov.:
31
AF XY:
0.374
AC XY:
27792
AN XY:
74228
show subpopulations
Gnomad4 AFR
AF:
0.414
Gnomad4 AMR
AF:
0.277
Gnomad4 ASJ
AF:
0.420
Gnomad4 EAS
AF:
0.228
Gnomad4 SAS
AF:
0.362
Gnomad4 FIN
AF:
0.320
Gnomad4 NFE
AF:
0.408
Gnomad4 OTH
AF:
0.352
Alfa
AF:
0.250
Hom.:
586
Bravo
AF:
0.378
Asia WGS
AF:
0.296
AC:
1035
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.22
Dann
Benign
0.32

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: rs2590712; hg19: chr12-54287445; API