rs6864913

Variant summary

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

The ENST00000522189.1(ENSG00000253693):​n.21+131916G>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 0.256 in 152,010 control chromosomes in the GnomAD database, including 5,696 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 ( 5696 hom., cov: 32)

Consequence


ENST00000522189.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20
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=-0.71).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000522189.1 linkuse as main transcriptn.21+131916G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.256
AC:
38936
AN:
151892
Hom.:
5694
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.417
Gnomad AMR
AF:
0.310
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.449
Gnomad SAS
AF:
0.419
Gnomad FIN
AF:
0.376
Gnomad MID
AF:
0.210
Gnomad NFE
AF:
0.273
Gnomad OTH
AF:
0.270
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.256
AC:
38950
AN:
152010
Hom.:
5696
Cov.:
32
AF XY:
0.266
AC XY:
19784
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.311
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.449
Gnomad4 SAS
AF:
0.418
Gnomad4 FIN
AF:
0.376
Gnomad4 NFE
AF:
0.273
Gnomad4 OTH
AF:
0.267
Alfa
AF:
0.275
Hom.:
12312
Bravo
AF:
0.248
Asia WGS
AF:
0.406
AC:
1413
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.71
CADD
Benign
15
DANN
Benign
0.73

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: rs6864913; hg19: chr5-164907971; API