rs1632344

Variant summary

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

The ENST00000424506.1(ENSG00000231143):​n.30+7305A>C 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 0.249 in 151,964 control chromosomes in the GnomAD database, including 5,005 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 0.25 ( 5005 hom., cov: 32)

Consequence


ENST00000424506.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.939
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 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
ENST00000424506.1 linkuse as main transcriptn.30+7305A>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.249
AC:
37796
AN:
151846
Hom.:
4982
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.309
Gnomad AMI
AF:
0.464
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.248
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.243
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.239
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.249
AC:
37864
AN:
151964
Hom.:
5005
Cov.:
32
AF XY:
0.245
AC XY:
18192
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.310
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.248
Gnomad4 EAS
AF:
0.106
Gnomad4 SAS
AF:
0.209
Gnomad4 FIN
AF:
0.243
Gnomad4 NFE
AF:
0.239
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.237
Hom.:
751
Bravo
AF:
0.247
Asia WGS
AF:
0.185
AC:
645
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.59

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: rs1632344; hg19: chr6-94880972; API