6-28808205-G-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 0.556 in 152,058 control chromosomes in the GnomAD database, including 24,528 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 0.56 ( 24528 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.81
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 (AFR) allele frequency at 95% confidence interval = 0.713 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:
0.555
AC:
84387
AN:
151940
Hom.:
24483
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.719
Gnomad AMI
AF:
0.643
Gnomad AMR
AF:
0.538
Gnomad ASJ
AF:
0.514
Gnomad EAS
AF:
0.629
Gnomad SAS
AF:
0.539
Gnomad FIN
AF:
0.406
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.546
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.556
AC:
84484
AN:
152058
Hom.:
24528
Cov.:
32
AF XY:
0.553
AC XY:
41121
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.720
Gnomad4 AMR
AF:
0.538
Gnomad4 ASJ
AF:
0.514
Gnomad4 EAS
AF:
0.631
Gnomad4 SAS
AF:
0.540
Gnomad4 FIN
AF:
0.406
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.541
Alfa
AF:
0.501
Hom.:
2462
Bravo
AF:
0.577
Asia WGS
AF:
0.543
AC:
1889
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.54
DANN
Benign
0.54

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: rs1011094; hg19: chr6-28775982; API