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GeneBe

rs11568820

chr12-47908762-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000395324.6(VDR):c.-83-25988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151972 control chromosomes in the gnomAD Genomes database, including 16322 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 0.38 ( 16322 hom., cov: 31)

Consequence

VDR
ENST00000395324.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.203

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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
VDRENST00000395324.6 linkuse as main transcriptc.-83-25988G>A intron_variant 5 P1P11473-1

Frequencies

GnomAD3 genomes
AF:
0.378
AC:
57431
AN:
151972
Hom.:
16322
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.800
Gnomad AMI
AF:
0.172
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.423
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.155
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.199
Gnomad OTH
AF:
0.354
Alfa
AF:
0.281
Hom.:
3191
Bravo
AF:
0.403
Asia WGS
AF:
0.386
AC:
1341
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.66
Dann
Benign
0.17

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: rs11568820; hg19: chr12-48302545;