7-119932337-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.835 in 151,886 control chromosomes in the GnomAD database, including 53,530 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 0.84 ( 53530 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.158
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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:
0.835
AC:
126708
AN:
151768
Hom.:
53466
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.952
Gnomad AMI
AF:
0.685
Gnomad AMR
AF:
0.825
Gnomad ASJ
AF:
0.763
Gnomad EAS
AF:
0.998
Gnomad SAS
AF:
0.817
Gnomad FIN
AF:
0.757
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.773
Gnomad OTH
AF:
0.830
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
126834
AN:
151886
Hom.:
53530
Cov.:
30
AF XY:
0.834
AC XY:
61863
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.952
Gnomad4 AMR
AF:
0.825
Gnomad4 ASJ
AF:
0.763
Gnomad4 EAS
AF:
0.998
Gnomad4 SAS
AF:
0.817
Gnomad4 FIN
AF:
0.757
Gnomad4 NFE
AF:
0.773
Gnomad4 OTH
AF:
0.832
Alfa
AF:
0.786
Hom.:
46757
Bravo
AF:
0.845
Asia WGS
AF:
0.926
AC:
3210
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.5
DANN
Benign
0.50

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10231641; hg19: chr7-119572391; API