7-86284446-T-C

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 0.741 in 151,902 control chromosomes in the GnomAD database, including 42,661 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 0.74 ( 42661 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48
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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.903 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:
0.741
AC:
112430
AN:
151784
Hom.:
42622
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.755
Gnomad AMR
AF:
0.806
Gnomad ASJ
AF:
0.863
Gnomad EAS
AF:
0.924
Gnomad SAS
AF:
0.926
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.771
Gnomad NFE
AF:
0.798
Gnomad OTH
AF:
0.771
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.741
AC:
112511
AN:
151902
Hom.:
42661
Cov.:
31
AF XY:
0.740
AC XY:
54964
AN XY:
74242
show subpopulations
Gnomad4 AFR
AF:
0.589
Gnomad4 AMR
AF:
0.807
Gnomad4 ASJ
AF:
0.863
Gnomad4 EAS
AF:
0.924
Gnomad4 SAS
AF:
0.925
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.798
Gnomad4 OTH
AF:
0.775
Alfa
AF:
0.791
Hom.:
21758
Bravo
AF:
0.742
Asia WGS
AF:
0.896
AC:
3104
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
8.1
DANN
Benign
0.67

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: rs2708553; hg19: chr7-85913762; API