rs2823322

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.355-6779C>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 0.225 in 152,080 control chromosomes in the GnomAD database, including 4,091 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 0.23 ( 4091 hom., cov: 32)

Consequence


ENST00000634644.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.214
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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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
ENST00000634644.1 linkuse as main transcriptn.355-6779C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34276
AN:
151962
Hom.:
4089
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.298
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.262
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.0783
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.203
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.188
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34294
AN:
152080
Hom.:
4091
Cov.:
32
AF XY:
0.226
AC XY:
16778
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.261
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.0783
Gnomad4 SAS
AF:
0.202
Gnomad4 FIN
AF:
0.203
Gnomad4 NFE
AF:
0.188
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.102
Hom.:
143
Bravo
AF:
0.234
Asia WGS
AF:
0.155
AC:
540
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.4
DANN
Benign
0.52

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: rs2823322; hg19: chr21-16893032; API