Variant chr21-42023389-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000455701.2(ZNF295-AS1):n.1307C>T 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 0.166 in 152,158 control chromosomes in the GnomAD database, including 2,218 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 0.17 ( 2218 hom., cov: 32)

Consequence

ZNF295-AS1
ENST00000455701.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.204

Variant links:

Genes affected

ZNF295-AS1 (HGNC:):

ZNF295-AS1 links:

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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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
ZNF295-AS1	NR_027273.2 linkuse as main transcript	n.163-917C>T	intron_variant
ZNF295-AS1	NR_119384.1 linkuse as main transcript	n.392-917C>T	intron_variant
ZNF295-AS1	NR_119385.1 linkuse as main transcript	n.209-917C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ZNF295-AS1	ENST00000412906.5 linkuse as main transcript	n.392-917C>T	intron_variant		1
ZNF295-AS1	ENST00000429739.1 linkuse as main transcript	n.165-917C>T	intron_variant		1
ZNF295-AS1	ENST00000455701.2 linkuse as main transcript	n.1307C>T	non_coding_transcript_exon_variant	1/1	2

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25245

AN:

152040

Hom.:

2218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.175

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.166

AC:

25271

AN:

152158

Hom.:

2218

Cov.:

AF XY:

0.168

AC XY:

12485

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.163

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.126

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.154

Hom.:

2586

Bravo

AF:

0.167

Asia WGS

AF:

0.199

AC:

691

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.56

DANN

Benign

0.33

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over