7-47703658-A-G

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 0.184 in 152,232 control chromosomes in the GnomAD database, including 3,079 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 ( 3079 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01
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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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:
0.184
AC:
28054
AN:
152112
Hom.:
3082
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0620
Gnomad AMI
AF:
0.225
Gnomad AMR
AF:
0.274
Gnomad ASJ
AF:
0.204
Gnomad EAS
AF:
0.363
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.196
Gnomad MID
AF:
0.208
Gnomad NFE
AF:
0.219
Gnomad OTH
AF:
0.171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.184
AC:
28060
AN:
152232
Hom.:
3079
Cov.:
32
AF XY:
0.187
AC XY:
13922
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.0619
Gnomad4 AMR
AF:
0.274
Gnomad4 ASJ
AF:
0.204
Gnomad4 EAS
AF:
0.363
Gnomad4 SAS
AF:
0.234
Gnomad4 FIN
AF:
0.196
Gnomad4 NFE
AF:
0.219
Gnomad4 OTH
AF:
0.172
Alfa
AF:
0.141
Hom.:
357
Bravo
AF:
0.185
Asia WGS
AF:
0.262
AC:
911
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.1
DANN
Benign
0.57

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: rs7791862; hg19: chr7-47743256; API