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GeneBe

rs12513663

Variant summary

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

The ENST00000503145.1(ENSG00000248296):​n.387-3774G>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 0.259 in 151,956 control chromosomes in the GnomAD database, including 6,490 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 0.26 ( 6490 hom., cov: 31)

Consequence


ENST00000503145.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436
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
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 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
ENST00000503145.1 linkuse as main transcriptn.387-3774G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39283
AN:
151838
Hom.:
6470
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0836
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.242
Gnomad EAS
AF:
0.618
Gnomad SAS
AF:
0.464
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.166
Gnomad NFE
AF:
0.278
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.259
AC:
39337
AN:
151956
Hom.:
6490
Cov.:
31
AF XY:
0.274
AC XY:
20342
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.0839
Gnomad4 AMR
AF:
0.381
Gnomad4 ASJ
AF:
0.242
Gnomad4 EAS
AF:
0.619
Gnomad4 SAS
AF:
0.463
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.278
Gnomad4 OTH
AF:
0.263
Alfa
AF:
0.257
Hom.:
866
Bravo
AF:
0.246
Asia WGS
AF:
0.532
AC:
1849
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.0
DANN
Benign
0.67

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: rs12513663; hg19: chr5-123832652; API