2-112996006-C-T

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 0.586 in 552,556 control chromosomes in the GnomAD database, including 98,823 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 0.54 ( 23582 hom., cov: 31)
Exomes 𝑓: 0.60 ( 75241 hom. )

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178
Variant links:
Genes affected

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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
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.112996006C>T intergenic_region
POLR2DP1 use as main transcriptn.112996006C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.543
AC:
82407
AN:
151886
Hom.:
23558
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.389
Gnomad AMI
AF:
0.516
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.893
Gnomad SAS
AF:
0.682
Gnomad FIN
AF:
0.721
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.546
Gnomad OTH
AF:
0.555
GnomAD4 exome
AF:
0.602
AC:
241324
AN:
400552
Hom.:
75241
AF XY:
0.604
AC XY:
128133
AN XY:
212208
show subpopulations
Gnomad4 AFR exome
AF:
0.383
Gnomad4 AMR exome
AF:
0.735
Gnomad4 ASJ exome
AF:
0.565
Gnomad4 EAS exome
AF:
0.883
Gnomad4 SAS exome
AF:
0.673
Gnomad4 FIN exome
AF:
0.708
Gnomad4 NFE exome
AF:
0.545
Gnomad4 OTH exome
AF:
0.580
GnomAD4 genome
AF:
0.543
AC:
82468
AN:
152004
Hom.:
23582
Cov.:
31
AF XY:
0.557
AC XY:
41360
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.389
Gnomad4 AMR
AF:
0.652
Gnomad4 ASJ
AF:
0.567
Gnomad4 EAS
AF:
0.893
Gnomad4 SAS
AF:
0.682
Gnomad4 FIN
AF:
0.721
Gnomad4 NFE
AF:
0.546
Gnomad4 OTH
AF:
0.558
Alfa
AF:
0.553
Hom.:
4053
Bravo
AF:
0.534
Asia WGS
AF:
0.750
AC:
2607
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.8
DANN
Benign
0.32

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: rs1374284; hg19: chr2-113753583; API