7-24502946-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 0.434 in 151,638 control chromosomes in the GnomAD database, including 14,675 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 0.43 ( 14675 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.04
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=-0.55).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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:
0.434
AC:
65689
AN:
151520
Hom.:
14645
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.405
Gnomad AMI
AF:
0.337
Gnomad AMR
AF:
0.447
Gnomad ASJ
AF:
0.358
Gnomad EAS
AF:
0.700
Gnomad SAS
AF:
0.646
Gnomad FIN
AF:
0.528
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.404
Gnomad OTH
AF:
0.416
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.434
AC:
65759
AN:
151638
Hom.:
14675
Cov.:
31
AF XY:
0.446
AC XY:
33008
AN XY:
74080
show subpopulations
Gnomad4 AFR
AF:
0.405
Gnomad4 AMR
AF:
0.448
Gnomad4 ASJ
AF:
0.358
Gnomad4 EAS
AF:
0.700
Gnomad4 SAS
AF:
0.649
Gnomad4 FIN
AF:
0.528
Gnomad4 NFE
AF:
0.404
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.360
Hom.:
2189
Bravo
AF:
0.427
Asia WGS
AF:
0.654
AC:
2267
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
12
DANN
Benign
0.47

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: rs4719772; hg19: chr7-24542565; API