rs232658

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-32634G>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 0.41 in 151,806 control chromosomes in the GnomAD database, including 14,908 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 0.41 ( 14908 hom., cov: 31)

Consequence


ENST00000425900.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.201
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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
ENST00000425900.1 linkuse as main transcriptn.82-32634G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.410
AC:
62163
AN:
151686
Hom.:
14869
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.662
Gnomad AMI
AF:
0.231
Gnomad AMR
AF:
0.412
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.505
Gnomad SAS
AF:
0.250
Gnomad FIN
AF:
0.262
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.401
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.410
AC:
62265
AN:
151806
Hom.:
14908
Cov.:
31
AF XY:
0.407
AC XY:
30159
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.663
Gnomad4 AMR
AF:
0.412
Gnomad4 ASJ
AF:
0.343
Gnomad4 EAS
AF:
0.505
Gnomad4 SAS
AF:
0.250
Gnomad4 FIN
AF:
0.262
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.404
Alfa
AF:
0.216
Hom.:
546
Bravo
AF:
0.436
Asia WGS
AF:
0.411
AC:
1428
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.85
DANN
Benign
0.75

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: rs232658; hg19: chr20-7094370; API