rs2839452

Variant names:

• chr21-42045938-T-C
• rs2839452
• ENST00000669320.2:n.330-7961T>C

Variant summary

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

The ENST00000669320.2(ZNF295-AS1):​n.330-7961T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,044 control chromosomes in the GnomAD database, including 4,612 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 0.24 (4612 hom., cov: 31)
• Consequence: ZNF295-AS1 ENST00000669320.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 3 publications found

Genes affected

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

LOC107985502 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985502	XR_001755063.3	n.1324+3956T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF295-AS1	ENST00000669320.2	n.330-7961T>C		intron_variant	Intron 2 of 2
ZNF295-AS1	ENST00000676087.2	n.433-7961T>C		intron_variant	Intron 2 of 2
ZNF295-AS1	ENST00000676145.1	n.537+3956T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36163 AN: 151926 Hom.: 4610 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.238 AC: 36187 AN: 152044 Hom.: 4612 Cov.: 31 AF XY: 0.239 AC XY: 17745 AN XY: 74306

African (AFR) AF: 0.205 AC: 8495 AN: 41470

American (AMR) AF: 0.180 AC: 2749 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3472

East Asian (EAS) AF: 0.0511 AC: 265 AN: 5184

South Asian (SAS) AF: 0.219 AC: 1058 AN: 4824

European-Finnish (FIN) AF: 0.315 AC: 3325 AN: 10548

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18699 AN: 67948

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.256 Hom.: 22037

Bravo AF: 0.223

Asia WGS AF: 0.151 AC: 527 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	0.20
DANN	Benign	0.42
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2839452; hg19: chr21-43466047;