6-72483449-C-A

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 0.67 in 151,882 control chromosomes in the GnomAD database, including 35,631 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 0.67 ( 35631 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.192
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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:
0.670
AC:
101747
AN:
151764
Hom.:
35587
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.887
Gnomad AMI
AF:
0.586
Gnomad AMR
AF:
0.615
Gnomad ASJ
AF:
0.493
Gnomad EAS
AF:
0.547
Gnomad SAS
AF:
0.582
Gnomad FIN
AF:
0.657
Gnomad MID
AF:
0.516
Gnomad NFE
AF:
0.580
Gnomad OTH
AF:
0.643
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.670
AC:
101833
AN:
151882
Hom.:
35631
Cov.:
31
AF XY:
0.669
AC XY:
49625
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.887
Gnomad4 AMR
AF:
0.614
Gnomad4 ASJ
AF:
0.493
Gnomad4 EAS
AF:
0.547
Gnomad4 SAS
AF:
0.582
Gnomad4 FIN
AF:
0.657
Gnomad4 NFE
AF:
0.580
Gnomad4 OTH
AF:
0.637
Alfa
AF:
0.551
Hom.:
2693
Bravo
AF:
0.674
Asia WGS
AF:
0.574
AC:
1999
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.77
DANN
Benign
0.60

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: rs1334346; hg19: chr6-73193151; API