chr1-193656103-G-C

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.154-17107G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,102 control chromosomes in the GnomAD database, including 2,615 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 0.18 ( 2615 hom., cov: 32)

Consequence

ENSG00000227240
ENST00000656143.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610

Publications

9 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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124904475XR_007066777.1 linkn.5234+182727G>C intron_variant Intron 3 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000227240ENST00000656143.2 linkn.154-17107G>C intron_variant Intron 1 of 5

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27303
AN:
151984
Hom.:
2612
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.205
Gnomad AMI
AF:
0.185
Gnomad AMR
AF:
0.125
Gnomad ASJ
AF:
0.190
Gnomad EAS
AF:
0.0256
Gnomad SAS
AF:
0.212
Gnomad FIN
AF:
0.197
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.182
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.180
AC:
27324
AN:
152102
Hom.:
2615
Cov.:
32
AF XY:
0.178
AC XY:
13227
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.205
AC:
8505
AN:
41488
American (AMR)
AF:
0.125
AC:
1910
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.190
AC:
661
AN:
3472
East Asian (EAS)
AF:
0.0257
AC:
133
AN:
5178
South Asian (SAS)
AF:
0.212
AC:
1025
AN:
4826
European-Finnish (FIN)
AF:
0.197
AC:
2076
AN:
10556
Middle Eastern (MID)
AF:
0.238
AC:
70
AN:
294
European-Non Finnish (NFE)
AF:
0.182
AC:
12390
AN:
67988
Other (OTH)
AF:
0.182
AC:
385
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1147
2293
3440
4586
5733
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
298
596
894
1192
1490
<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:
0.0985
Hom.:
167
Bravo
AF:
0.171
Asia WGS
AF:
0.137
AC:
477
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.3
DANN
Benign
0.42
PhyloP100
0.061

Splicing

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

Publications

Other links and lift over

dbSNP: rs6678275; hg19: chr1-193625233; API