chr2-170684313-A-C

Variant summary

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

The ENST00000428156.1(ENSG00000213981):​n.389-1254T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,020 control chromosomes in the GnomAD database, including 10,752 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 ( 10752 hom., cov: 32)

Consequence

ENSG00000213981
ENST00000428156.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00200

Publications

18 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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC100130256NR_187617.1 linkn.145-1254T>G intron_variant Intron 1 of 14
LOC100130256NR_187618.1 linkn.145-1254T>G intron_variant Intron 1 of 13
LOC100130256NR_187619.1 linkn.145-1254T>G intron_variant Intron 1 of 11

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000213981ENST00000428156.1 linkn.389-1254T>G intron_variant Intron 1 of 9 2

Frequencies

GnomAD3 genomes
AF:
0.371
AC:
56361
AN:
151902
Hom.:
10729
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.358
Gnomad AMI
AF:
0.309
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.291
Gnomad EAS
AF:
0.285
Gnomad SAS
AF:
0.391
Gnomad FIN
AF:
0.386
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.356
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.371
AC:
56427
AN:
152020
Hom.:
10752
Cov.:
32
AF XY:
0.373
AC XY:
27702
AN XY:
74308
show subpopulations
African (AFR)
AF:
0.358
AC:
14864
AN:
41488
American (AMR)
AF:
0.508
AC:
7749
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.291
AC:
1010
AN:
3468
East Asian (EAS)
AF:
0.285
AC:
1472
AN:
5166
South Asian (SAS)
AF:
0.390
AC:
1879
AN:
4822
European-Finnish (FIN)
AF:
0.386
AC:
4078
AN:
10554
Middle Eastern (MID)
AF:
0.306
AC:
90
AN:
294
European-Non Finnish (NFE)
AF:
0.356
AC:
24226
AN:
67956
Other (OTH)
AF:
0.370
AC:
779
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1817
3633
5450
7266
9083
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
540
1080
1620
2160
2700
<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:
0.359
Hom.:
33964
Bravo
AF:
0.383
Asia WGS
AF:
0.357
AC:
1239
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
4.6
DANN
Benign
0.73
PhyloP100
0.0020

Splicing

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

Publications

Other links and lift over

dbSNP: rs2080401; hg19: chr2-171540823; API