1-237940201-C-T

Variant summary

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

The variant allele was found at a frequency of 0.534 in 151,860 control chromosomes in the GnomAD database, including 22,473 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 0.53 ( 22473 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

Publications

16 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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

Frequencies

GnomAD3 genomes
AF:
0.533
AC:
80947
AN:
151742
Hom.:
22436
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.700
Gnomad AMI
AF:
0.466
Gnomad AMR
AF:
0.482
Gnomad ASJ
AF:
0.430
Gnomad EAS
AF:
0.518
Gnomad SAS
AF:
0.550
Gnomad FIN
AF:
0.530
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.500
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.534
AC:
81029
AN:
151860
Hom.:
22473
Cov.:
31
AF XY:
0.540
AC XY:
40042
AN XY:
74214
show subpopulations
African (AFR)
AF:
0.700
AC:
28996
AN:
41416
American (AMR)
AF:
0.482
AC:
7351
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.430
AC:
1493
AN:
3470
East Asian (EAS)
AF:
0.518
AC:
2663
AN:
5142
South Asian (SAS)
AF:
0.547
AC:
2635
AN:
4814
European-Finnish (FIN)
AF:
0.530
AC:
5579
AN:
10528
Middle Eastern (MID)
AF:
0.418
AC:
123
AN:
294
European-Non Finnish (NFE)
AF:
0.452
AC:
30706
AN:
67912
Other (OTH)
AF:
0.502
AC:
1060
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1863
3726
5589
7452
9315
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
690
1380
2070
2760
3450
<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:
0.470
Hom.:
79945
Bravo
AF:
0.532
Asia WGS
AF:
0.589
AC:
2047
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.23
DANN
Benign
0.74
PhyloP100
-2.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs2499604; hg19: chr1-238103501; API