21-42039063-T-C

Variant names:

• chr21-42039063-T-C
• rs220245
• ENST00000669320.1:n.323+7539T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669320.1(ZNF295-AS1):​n.323+7539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 152,108 control chromosomes in the GnomAD database, including 36,899 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 0.65 (36899 hom., cov: 32)
• Consequence: ZNF295-AS1 ENST00000669320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF295-AS1	ENST00000669320.1	n.323+7539T>C		intron_variant	Intron 2 of 2
ZNF295-AS1	ENST00000676087.1	n.232+7539T>C		intron_variant	Intron 2 of 2
ZNF295-AS1	ENST00000676145.1	n.72-2454T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98946 AN: 151990 Hom.: 36896 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.651 AC: 98965 AN: 152108 Hom.: 36899 Cov.: 32 AF XY: 0.658 AC XY: 48927 AN XY: 74360

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.851

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.674

Alfa AF: 0.791 Hom.: 101961

Bravo AF: 0.627

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs220245; hg19: chr21-43459172;