chr8-75571621-C-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 0.663 in 152,026 control chromosomes in the GnomAD database, including 34,812 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 0.66 ( 34812 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.10
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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:
0.663
AC:
100734
AN:
151908
Hom.:
34779
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.838
Gnomad AMI
AF:
0.678
Gnomad AMR
AF:
0.495
Gnomad ASJ
AF:
0.560
Gnomad EAS
AF:
0.400
Gnomad SAS
AF:
0.551
Gnomad FIN
AF:
0.729
Gnomad MID
AF:
0.589
Gnomad NFE
AF:
0.618
Gnomad OTH
AF:
0.640
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.663
AC:
100818
AN:
152026
Hom.:
34812
Cov.:
31
AF XY:
0.661
AC XY:
49146
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.838
Gnomad4 AMR
AF:
0.494
Gnomad4 ASJ
AF:
0.560
Gnomad4 EAS
AF:
0.400
Gnomad4 SAS
AF:
0.549
Gnomad4 FIN
AF:
0.729
Gnomad4 NFE
AF:
0.618
Gnomad4 OTH
AF:
0.640
Alfa
AF:
0.569
Hom.:
4786
Bravo
AF:
0.649
Asia WGS
AF:
0.495
AC:
1720
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.070
DANN
Benign
0.79

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: rs1399564; hg19: chr8-76483856; API