rs1723623

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.439-27569C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,530 control chromosomes in the GnomAD database, including 19,373 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 0.50 ( 19373 hom., cov: 30)

Consequence

ENSG00000226965
ENST00000658032.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.517

Publications

1 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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000226965ENST00000658032.1 linkn.439-27569C>T intron_variant Intron 5 of 5
ENSG00000226965ENST00000667232.1 linkn.520-27569C>T intron_variant Intron 6 of 7
ENSG00000226965ENST00000755897.1 linkn.34-29940C>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.499
AC:
75546
AN:
151412
Hom.:
19364
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.405
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.506
Gnomad ASJ
AF:
0.343
Gnomad EAS
AF:
0.321
Gnomad SAS
AF:
0.456
Gnomad FIN
AF:
0.542
Gnomad MID
AF:
0.379
Gnomad NFE
AF:
0.575
Gnomad OTH
AF:
0.485
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.499
AC:
75582
AN:
151530
Hom.:
19373
Cov.:
30
AF XY:
0.496
AC XY:
36741
AN XY:
74022
show subpopulations
African (AFR)
AF:
0.405
AC:
16723
AN:
41304
American (AMR)
AF:
0.506
AC:
7693
AN:
15200
Ashkenazi Jewish (ASJ)
AF:
0.343
AC:
1187
AN:
3464
East Asian (EAS)
AF:
0.321
AC:
1643
AN:
5120
South Asian (SAS)
AF:
0.457
AC:
2194
AN:
4804
European-Finnish (FIN)
AF:
0.542
AC:
5704
AN:
10526
Middle Eastern (MID)
AF:
0.356
AC:
104
AN:
292
European-Non Finnish (NFE)
AF:
0.575
AC:
38967
AN:
67812
Other (OTH)
AF:
0.480
AC:
1008
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1844
3688
5533
7377
9221
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
688
1376
2064
2752
3440
<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:
0.535
Hom.:
2768
Bravo
AF:
0.490
Asia WGS
AF:
0.356
AC:
1236
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.73
DANN
Benign
0.50
PhyloP100
0.52

Splicing

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

Publications

Other links and lift over

dbSNP: rs1723623; hg19: chr7-109778327; API