GeneBe

2-142877384-A-G

Variant names:

Variant summary

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

The ENST00000797297.1(ENSG00000303809):​n.66+62T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,472 control chromosomes in the GnomAD database, including 23,495 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 0.55 ( 23495 hom., cov: 31)
Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

ENSG00000303809
ENST00000797297.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.775

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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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
ENSG00000303809ENST00000797297.1 linkn.66+62T>C intron_variant Intron 1 of 5
ENSG00000303809ENST00000797298.1 linkn.68+62T>C intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.545
AC:
82543
AN:
151352
Hom.:
23455
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.699
Gnomad AMI
AF:
0.521
Gnomad AMR
AF:
0.595
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.547
Gnomad SAS
AF:
0.681
Gnomad FIN
AF:
0.508
Gnomad MID
AF:
0.394
Gnomad NFE
AF:
0.445
Gnomad OTH
AF:
0.504
GnomAD4 exome
AF:
0.250
AC:
1
AN:
4
Hom.:
0
AF XY:
0.250
AC XY:
1
AN XY:
4
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.250
AC:
1
AN:
4
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.546
AC:
82632
AN:
151468
Hom.:
23495
Cov.:
31
AF XY:
0.552
AC XY:
40868
AN XY:
74004
show subpopulations
African (AFR)
AF:
0.699
AC:
28835
AN:
41274
American (AMR)
AF:
0.596
AC:
9071
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
0.423
AC:
1462
AN:
3458
East Asian (EAS)
AF:
0.547
AC:
2807
AN:
5128
South Asian (SAS)
AF:
0.683
AC:
3292
AN:
4822
European-Finnish (FIN)
AF:
0.508
AC:
5323
AN:
10484
Middle Eastern (MID)
AF:
0.386
AC:
112
AN:
290
European-Non Finnish (NFE)
AF:
0.445
AC:
30190
AN:
67784
Other (OTH)
AF:
0.510
AC:
1069
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1831
3663
5494
7326
9157
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
708
1416
2124
2832
3540
<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:
0.499
Hom.:
3145
Bravo
AF:
0.560
Asia WGS
AF:
0.646
AC:
2245
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.50
DANN
Benign
0.52
PhyloP100
-0.78
PromoterAI
-0.055
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1465839; hg19: chr2-143634953; API