rs10425253

Variant summary

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

The ENST00000585364.1(ENSG00000267081):​n.106+4548G>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 0.213 in 152,148 control chromosomes in the GnomAD database, including 3,914 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 0.21 ( 3914 hom., cov: 33)

Consequence


ENST00000585364.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 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
ENST00000585364.1 linkuse as main transcriptn.106+4548G>A intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.213
AC:
32387
AN:
152030
Hom.:
3912
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.355
Gnomad AMR
AF:
0.155
Gnomad ASJ
AF:
0.235
Gnomad EAS
AF:
0.0162
Gnomad SAS
AF:
0.0766
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.281
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.213
AC:
32397
AN:
152148
Hom.:
3914
Cov.:
33
AF XY:
0.204
AC XY:
15172
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.163
Gnomad4 AMR
AF:
0.155
Gnomad4 ASJ
AF:
0.235
Gnomad4 EAS
AF:
0.0162
Gnomad4 SAS
AF:
0.0763
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.281
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.259
Hom.:
652
Bravo
AF:
0.208
Asia WGS
AF:
0.0680
AC:
236
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.6
DANN
Benign
0.46

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: rs10425253; hg19: chr19-31346535; API