rs6673928

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 0.196 in 152,156 control chromosomes in the GnomAD database, including 3,440 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 0.20 ( 3440 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.181
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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:
0.196
AC:
29754
AN:
152036
Hom.:
3439
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.118
Gnomad AMI
AF:
0.290
Gnomad AMR
AF:
0.153
Gnomad ASJ
AF:
0.186
Gnomad EAS
AF:
0.00424
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.243
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.267
Gnomad OTH
AF:
0.168
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29756
AN:
152156
Hom.:
3440
Cov.:
32
AF XY:
0.190
AC XY:
14167
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.118
Gnomad4 AMR
AF:
0.153
Gnomad4 ASJ
AF:
0.186
Gnomad4 EAS
AF:
0.00425
Gnomad4 SAS
AF:
0.107
Gnomad4 FIN
AF:
0.243
Gnomad4 NFE
AF:
0.267
Gnomad4 OTH
AF:
0.166
Alfa
AF:
0.236
Hom.:
940
Bravo
AF:
0.186
Asia WGS
AF:
0.0610
AC:
215
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
8.8
DANN
Benign
0.86

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: rs6673928; hg19: chr1-206937245; API