chr6-66673715-A-G

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 0.302 in 151,988 control chromosomes in the GnomAD database, including 7,197 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 0.30 ( 7197 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.488
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=-0.73).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.302
AC:
45845
AN:
151870
Hom.:
7184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.252
Gnomad AMI
AF:
0.240
Gnomad AMR
AF:
0.401
Gnomad ASJ
AF:
0.262
Gnomad EAS
AF:
0.156
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.364
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.323
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.302
AC:
45891
AN:
151988
Hom.:
7197
Cov.:
32
AF XY:
0.306
AC XY:
22765
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.252
Gnomad4 AMR
AF:
0.402
Gnomad4 ASJ
AF:
0.262
Gnomad4 EAS
AF:
0.157
Gnomad4 SAS
AF:
0.272
Gnomad4 FIN
AF:
0.364
Gnomad4 NFE
AF:
0.316
Gnomad4 OTH
AF:
0.323
Alfa
AF:
0.310
Hom.:
933
Bravo
AF:
0.302
Asia WGS
AF:
0.232
AC:
810
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
13
DANN
Benign
0.87

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: rs1455085; hg19: chr6-67383608; API