6-32232370-C-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 0.336 in 147,438 control chromosomes in the GnomAD database, including 8,800 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 0.34 ( 8800 hom., cov: 25)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.505
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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 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:
0.336
AC:
49477
AN:
147320
Hom.:
8794
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.317
Gnomad AMI
AF:
0.316
Gnomad AMR
AF:
0.436
Gnomad ASJ
AF:
0.679
Gnomad EAS
AF:
0.395
Gnomad SAS
AF:
0.382
Gnomad FIN
AF:
0.209
Gnomad MID
AF:
0.448
Gnomad NFE
AF:
0.315
Gnomad OTH
AF:
0.402
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.336
AC:
49518
AN:
147438
Hom.:
8800
Cov.:
25
AF XY:
0.335
AC XY:
23937
AN XY:
71422
show subpopulations
Gnomad4 AFR
AF:
0.317
Gnomad4 AMR
AF:
0.436
Gnomad4 ASJ
AF:
0.679
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.383
Gnomad4 FIN
AF:
0.209
Gnomad4 NFE
AF:
0.315
Gnomad4 OTH
AF:
0.406
Alfa
AF:
0.166
Hom.:
320
Bravo
AF:
0.347
Asia WGS
AF:
0.427
AC:
1479
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
5.7
DANN
Benign
0.64

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: rs3134926; hg19: chr6-32200147; API