21-42023389-C-T

Variant names:

• chr21-42023389-C-T
• rs2839440
• ENST00000412906.6:n.438-917C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 13 publications found

Genes affected

ZNF295-AS1 (HGNC:23130): (ZNF295 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF295-AS1	NR_027273.2		n.163-917C>T		intron	N/A
	ZNF295-AS1	NR_119384.1		n.392-917C>T		intron	N/A
	ZNF295-AS1	NR_119385.1		n.209-917C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF295-AS1	ENST00000412906.6	TSL:1	n.438-917C>T		intron	N/A
	ZNF295-AS1	ENST00000429739.2	TSL:1	n.185-917C>T		intron	N/A
	ZNF295-AS1	ENST00000455701.2	TSL:2	n.1307C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25245 AN: 152040 Hom.: 2218 Cov.: 32

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.: 32 AF XY: 0.168 AC XY: 12485 AN XY: 74384

African (AFR) AF: 0.163 AC: 6775 AN: 41510

American (AMR) AF: 0.174 AC: 2660 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1650 AN: 5166

South Asian (SAS) AF: 0.126 AC: 609 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1846 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10616 AN: 68002

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.157 Hom.: 3862

Bravo AF: 0.167

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2839440; hg19: chr21-43443498;