7-82703579-G-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 0.0575 in 152,136 control chromosomes in the GnomAD database, including 326 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 0.057 ( 326 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.368
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 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:
0.0576
AC:
8750
AN:
152018
Hom.:
325
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0156
Gnomad AMI
AF:
0.109
Gnomad AMR
AF:
0.0593
Gnomad ASJ
AF:
0.0917
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.0321
Gnomad FIN
AF:
0.0471
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0872
Gnomad OTH
AF:
0.0796
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0575
AC:
8746
AN:
152136
Hom.:
326
Cov.:
32
AF XY:
0.0549
AC XY:
4086
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0155
Gnomad4 AMR
AF:
0.0592
Gnomad4 ASJ
AF:
0.0917
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0313
Gnomad4 FIN
AF:
0.0471
Gnomad4 NFE
AF:
0.0872
Gnomad4 OTH
AF:
0.0787
Alfa
AF:
0.0675
Hom.:
197
Bravo
AF:
0.0578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.39
DANN
Benign
0.26

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: rs10486980; hg19: chr7-82332895; API