21-42039063-T-C

Position:

• chr21-42039063-T-C

Variant summary

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

The ENST00000676087.1(ZNF295-AS1):​n.232+7539T>C variant causes a intron, non coding transcript 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 ENST00000676087.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF295-AS1	ENST00000676087.1	n.232+7539T>C		intron_variant, non_coding_transcript_variant
ZNF295-AS1	ENST00000669320.1	n.323+7539T>C		intron_variant, non_coding_transcript_variant
ZNF295-AS1	ENST00000676145.1	n.72-2454T>C		intron_variant, non_coding_transcript_variant

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;