chr1-159725971-A-G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,198 control chromosomes in the GnomAD database, including 847 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 0.093 ( 847 hom., cov: 32)

Consequence

ENSG00000297913
ENST00000751816.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.410

Publications

3 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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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
ENSG00000297913ENST00000751816.1 linkn.108-556A>G intron_variant Intron 1 of 2
ENSG00000297913ENST00000751817.1 linkn.110-556A>G intron_variant Intron 1 of 3
ENSG00000297913ENST00000751818.1 linkn.63-556A>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.0932
AC:
14174
AN:
152080
Hom.:
845
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0224
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.0935
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.0344
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.129
Gnomad OTH
AF:
0.0997
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0932
AC:
14178
AN:
152198
Hom.:
847
Cov.:
32
AF XY:
0.0941
AC XY:
7001
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.0224
AC:
929
AN:
41552
American (AMR)
AF:
0.0934
AC:
1426
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.133
AC:
461
AN:
3472
East Asian (EAS)
AF:
0.0343
AC:
178
AN:
5184
South Asian (SAS)
AF:
0.102
AC:
492
AN:
4824
European-Finnish (FIN)
AF:
0.149
AC:
1581
AN:
10592
Middle Eastern (MID)
AF:
0.0816
AC:
24
AN:
294
European-Non Finnish (NFE)
AF:
0.129
AC:
8781
AN:
67986
Other (OTH)
AF:
0.0996
AC:
210
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
631
1262
1892
2523
3154
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
158
316
474
632
790
<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:
0.111
Hom.:
1702
Bravo
AF:
0.0853
Asia WGS
AF:
0.0600
AC:
209
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.1
DANN
Benign
0.78
PhyloP100
0.41

Splicing

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

Publications

Other links and lift over

dbSNP: rs3116654; hg19: chr1-159695761; API