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GeneBe

rs12515335

Positions:

Variant summary

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

The ENST00000657075.1(ENSG00000249782):​n.689-3102T>C 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 0.187 in 152,058 control chromosomes in the GnomAD database, including 3,063 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 0.19 ( 3063 hom., cov: 32)

Consequence


ENST00000657075.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.443
Variant links:
Genes affected

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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=-0.9).
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 = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105374647XR_925766.3 linkuse as main transcriptn.651-3102T>C intron_variant, non_coding_transcript_variant
LOC105374647XR_925767.3 linkuse as main transcriptn.641-3102T>C intron_variant, non_coding_transcript_variant
LOC105374647XR_925768.3 linkuse as main transcriptn.473-3102T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000657075.1 linkuse as main transcriptn.689-3102T>C intron_variant, non_coding_transcript_variant
ENST00000654467.1 linkuse as main transcriptn.472-3102T>C intron_variant, non_coding_transcript_variant
ENST00000659580.1 linkuse as main transcriptn.651-3102T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.187
AC:
28456
AN:
151940
Hom.:
3062
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.116
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.170
Gnomad ASJ
AF:
0.232
Gnomad EAS
AF:
0.0137
Gnomad SAS
AF:
0.0966
Gnomad FIN
AF:
0.224
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.246
Gnomad OTH
AF:
0.217
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:
0.187
AC:
28479
AN:
152058
Hom.:
3063
Cov.:
32
AF XY:
0.184
AC XY:
13645
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.116
Gnomad4 AMR
AF:
0.170
Gnomad4 ASJ
AF:
0.232
Gnomad4 EAS
AF:
0.0137
Gnomad4 SAS
AF:
0.0971
Gnomad4 FIN
AF:
0.224
Gnomad4 NFE
AF:
0.246
Gnomad4 OTH
AF:
0.218
Alfa
AF:
0.219
Hom.:
2770
Bravo
AF:
0.181
Asia WGS
AF:
0.0680
AC:
236
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.3
DANN
Benign
0.74

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: rs12515335; hg19: chr5-8557087; API