rs6973392

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 0.164 in 152,088 control chromosomes in the GnomAD database, including 3,270 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 0.16 ( 3270 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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:
0.163
AC:
24817
AN:
151970
Hom.:
3254
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.356
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.118
Gnomad ASJ
AF:
0.235
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.152
Gnomad FIN
AF:
0.0354
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.0781
Gnomad OTH
AF:
0.182
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.164
AC:
24882
AN:
152088
Hom.:
3270
Cov.:
32
AF XY:
0.160
AC XY:
11896
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.357
Gnomad4 AMR
AF:
0.118
Gnomad4 ASJ
AF:
0.235
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.150
Gnomad4 FIN
AF:
0.0354
Gnomad4 NFE
AF:
0.0781
Gnomad4 OTH
AF:
0.185
Alfa
AF:
0.125
Hom.:
317
Bravo
AF:
0.181
Asia WGS
AF:
0.168
AC:
583
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
1.3
DANN
Benign
0.47

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: rs6973392; hg19: chr7-89060733; API