rs5965083

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 0.296 in 111,537 control chromosomes in the GnomAD database, including 6,398 homozygotes. There are 9,415 hemizygotes in GnomAD. 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 ( 6398 hom., 9415 hem., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.14
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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:
0.296
AC:
32966
AN:
111486
Hom.:
6394
Cov.:
23
AF XY:
0.277
AC XY:
9361
AN XY:
33734
show subpopulations
Gnomad AFR
AF:
0.722
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.206
Gnomad ASJ
AF:
0.108
Gnomad EAS
AF:
0.000560
Gnomad SAS
AF:
0.0833
Gnomad FIN
AF:
0.118
Gnomad MID
AF:
0.151
Gnomad NFE
AF:
0.131
Gnomad OTH
AF:
0.236
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.296
AC:
33027
AN:
111537
Hom.:
6398
Cov.:
23
AF XY:
0.279
AC XY:
9415
AN XY:
33795
show subpopulations
Gnomad4 AFR
AF:
0.722
Gnomad4 AMR
AF:
0.206
Gnomad4 ASJ
AF:
0.108
Gnomad4 EAS
AF:
0.000562
Gnomad4 SAS
AF:
0.0857
Gnomad4 FIN
AF:
0.118
Gnomad4 NFE
AF:
0.131
Gnomad4 OTH
AF:
0.236
Alfa
AF:
0.149
Hom.:
7838
Bravo
AF:
0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.018
DANN
Benign
0.57

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: rs5965083; hg19: chrX-65230426; API