chr5-173506839-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000827042.1(ENSG00000253968):​n.446+467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,842 control chromosomes in the GnomAD database, including 10,435 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 0.37 ( 10435 hom., cov: 31)

Consequence

ENSG00000253968
ENST00000827042.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

2 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105377732XR_001743001.1 linkn.2862+467G>A intron_variant Intron 13 of 14
LOC105377732XR_007059057.1 linkn.3922+467G>A intron_variant Intron 16 of 17

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000253968ENST00000827042.1 linkn.446+467G>A intron_variant Intron 2 of 2
ENSG00000253968ENST00000827044.1 linkn.374+467G>A intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.366
AC:
55572
AN:
151724
Hom.:
10412
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.294
Gnomad AMI
AF:
0.434
Gnomad AMR
AF:
0.463
Gnomad ASJ
AF:
0.329
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.402
Gnomad FIN
AF:
0.389
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.390
Gnomad OTH
AF:
0.389
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55641
AN:
151842
Hom.:
10435
Cov.:
31
AF XY:
0.370
AC XY:
27452
AN XY:
74220
show subpopulations
African (AFR)
AF:
0.294
AC:
12161
AN:
41384
American (AMR)
AF:
0.464
AC:
7080
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.329
AC:
1142
AN:
3470
East Asian (EAS)
AF:
0.272
AC:
1401
AN:
5150
South Asian (SAS)
AF:
0.403
AC:
1934
AN:
4798
European-Finnish (FIN)
AF:
0.389
AC:
4108
AN:
10552
Middle Eastern (MID)
AF:
0.306
AC:
90
AN:
294
European-Non Finnish (NFE)
AF:
0.390
AC:
26499
AN:
67916
Other (OTH)
AF:
0.394
AC:
831
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1763
3526
5290
7053
8816
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
554
1108
1662
2216
2770
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.389
Hom.:
6526
Bravo
AF:
0.368
Asia WGS
AF:
0.347
AC:
1209
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
3.7
DANN
Benign
0.73
PhyloP100
-0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7716959; hg19: chr5-172933842; COSMIC: COSV60232066; API