7-30931374-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 0.215 in 152,150 control chromosomes in the GnomAD database, including 3,727 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 0.21 ( 3727 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328

Publications

6 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=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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:
0.215
AC:
32653
AN:
152032
Hom.:
3724
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.154
Gnomad AMI
AF:
0.130
Gnomad AMR
AF:
0.236
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.100
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.182
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.255
Gnomad OTH
AF:
0.241
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.215
AC:
32672
AN:
152150
Hom.:
3727
Cov.:
32
AF XY:
0.213
AC XY:
15839
AN XY:
74374
show subpopulations
African (AFR)
AF:
0.154
AC:
6386
AN:
41508
American (AMR)
AF:
0.236
AC:
3604
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.252
AC:
874
AN:
3472
East Asian (EAS)
AF:
0.101
AC:
521
AN:
5170
South Asian (SAS)
AF:
0.267
AC:
1286
AN:
4818
European-Finnish (FIN)
AF:
0.182
AC:
1930
AN:
10590
Middle Eastern (MID)
AF:
0.320
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
0.255
AC:
17344
AN:
67984
Other (OTH)
AF:
0.243
AC:
514
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1319
2638
3957
5276
6595
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
334
668
1002
1336
1670
<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:
0.242
Hom.:
7925
Bravo
AF:
0.215
Asia WGS
AF:
0.237
AC:
822
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.0
DANN
Benign
0.78
PhyloP100
-0.33

Splicing

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

Publications

Other links and lift over

dbSNP: rs13222180; hg19: chr7-30970989; API