7-114082577-T-A

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 0.257 in 152,080 control chromosomes in the GnomAD database, including 5,423 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 0.26 ( 5423 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215
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=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.257
AC:
39007
AN:
151962
Hom.:
5424
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.248
Gnomad AMI
AF:
0.163
Gnomad AMR
AF:
0.217
Gnomad ASJ
AF:
0.353
Gnomad EAS
AF:
0.0166
Gnomad SAS
AF:
0.195
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.290
Gnomad OTH
AF:
0.278
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.257
AC:
39010
AN:
152080
Hom.:
5423
Cov.:
33
AF XY:
0.254
AC XY:
18866
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.248
Gnomad4 AMR
AF:
0.217
Gnomad4 ASJ
AF:
0.353
Gnomad4 EAS
AF:
0.0166
Gnomad4 SAS
AF:
0.193
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.290
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.171
Hom.:
398
Bravo
AF:
0.250
Asia WGS
AF:
0.139
AC:
485
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
8.0
DANN
Benign
0.72

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: rs7803667; hg19: chr7-113722632; API