Menu
GeneBe

rs7306498

chr12-53865917-G-Achr12-53865917-G-C

Variant summary

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

The ENST00000663306.1(ENSG00000286069):n.480-9238G>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 0.358 in 151,974 control chromosomes in the GnomAD database, including 10,041 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 0.36 ( 10041 hom., cov: 31)

Consequence


ENST00000663306.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07
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=-0.85).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107984525XR_002957415.2 linkuse as main transcriptn.451+15505G>A intron_variant, non_coding_transcript_variant
LOC107984525XR_001749153.2 linkuse as main transcriptn.282-9238G>A intron_variant, non_coding_transcript_variant
LOC107984525XR_007063319.1 linkuse as main transcriptn.1401-9238G>A intron_variant, non_coding_transcript_variant
LOC107984525XR_007063320.1 linkuse as main transcriptn.229-9238G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000663306.1 linkuse as main transcriptn.480-9238G>A intron_variant, non_coding_transcript_variant
ENST00000652339.1 linkuse as main transcriptn.509+5039G>A intron_variant, non_coding_transcript_variant
ENST00000654713.1 linkuse as main transcriptn.317+15505G>A intron_variant, non_coding_transcript_variant
ENST00000656247.1 linkuse as main transcriptn.344+15505G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.358
AC:
54440
AN:
151856
Hom.:
10039
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.333
Gnomad AMI
AF:
0.404
Gnomad AMR
AF:
0.262
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.229
Gnomad SAS
AF:
0.359
Gnomad FIN
AF:
0.320
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.338
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:
0.358
AC:
54451
AN:
151974
Hom.:
10041
Cov.:
31
AF XY:
0.351
AC XY:
26099
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.333
Gnomad4 AMR
AF:
0.262
Gnomad4 ASJ
AF:
0.420
Gnomad4 EAS
AF:
0.230
Gnomad4 SAS
AF:
0.359
Gnomad4 FIN
AF:
0.320
Gnomad4 NFE
AF:
0.408
Gnomad4 OTH
AF:
0.337
Alfa
AF:
0.280
Hom.:
985
Bravo
AF:
0.350
Asia WGS
AF:
0.288
AC:
1008
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
6.9
Dann
Benign
0.39

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: rs7306498; hg19: chr12-54259701; API