rs869538

Variant summary

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

The ENST00000515232.1(ENSG00000249022):​n.49+387C>T 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 0.306 in 151,978 control chromosomes in the GnomAD database, including 7,659 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 0.31 ( 7659 hom., cov: 32)

Consequence


ENST00000515232.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.225
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=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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
ENST00000515232.1 linkuse as main transcriptn.49+387C>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.306
AC:
46395
AN:
151858
Hom.:
7650
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.435
Gnomad ASJ
AF:
0.390
Gnomad EAS
AF:
0.383
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.250
Gnomad MID
AF:
0.341
Gnomad NFE
AF:
0.340
Gnomad OTH
AF:
0.348
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.306
AC:
46449
AN:
151978
Hom.:
7659
Cov.:
32
AF XY:
0.304
AC XY:
22576
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.436
Gnomad4 ASJ
AF:
0.390
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.250
Gnomad4 NFE
AF:
0.340
Gnomad4 OTH
AF:
0.344
Alfa
AF:
0.315
Hom.:
990
Bravo
AF:
0.321
Asia WGS
AF:
0.324
AC:
1126
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.7
DANN
Benign
0.66

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: rs869538; hg19: chr4-153955798; API