9-22118103-T-G

Variant summary

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

The ENST00000643286.1(CDKN2B-AS1):​n.516T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 152,384 control chromosomes in the GnomAD database, including 153 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 0.022 ( 153 hom., cov: 32)
Exomes 𝑓: 0.010 ( 0 hom. )

Consequence

CDKN2B-AS1
ENST00000643286.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.205
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CDKN2B-AS1NR_003529.4 linkuse as main transcriptn.2909-541T>G intron_variant
CDKN2B-AS1NR_047532.2 linkuse as main transcriptn.1698-541T>G intron_variant
CDKN2B-AS1NR_047534.2 linkuse as main transcriptn.962-541T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDKN2B-AS1ENST00000422420.2 linkuse as main transcriptn.135-2097T>G intron_variant 1
CDKN2B-AS1ENST00000428597.6 linkuse as main transcriptn.2909-541T>G intron_variant 1
CDKN2B-AS1ENST00000577551.5 linkuse as main transcriptn.610-541T>G intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.0218
AC:
3318
AN:
152164
Hom.:
153
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0446
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00681
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.188
Gnomad SAS
AF:
0.0682
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000456
Gnomad OTH
AF:
0.0143
GnomAD4 exome
AF:
0.0100
AC:
1
AN:
100
Hom.:
0
Cov.:
0
AF XY:
0.0161
AC XY:
1
AN XY:
62
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0218
AC:
3322
AN:
152284
Hom.:
153
Cov.:
32
AF XY:
0.0228
AC XY:
1698
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0445
Gnomad4 AMR
AF:
0.00680
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.188
Gnomad4 SAS
AF:
0.0683
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000456
Gnomad4 OTH
AF:
0.0151
Alfa
AF:
0.0127
Hom.:
12
Bravo
AF:
0.0231
Asia WGS
AF:
0.0890
AC:
308
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.6
DANN
Benign
0.71

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: rs17761446; hg19: chr9-22118102; API