chr21-42039063-T-C

Variant names:

• chr21-42039063-T-C
• rs220245
• ENST00000669320.2:n.329+7539T>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.329+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 ENST00000669320.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669320.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF295-AS1	ENST00000669320.2		n.329+7539T>C		intron	N/A
	ZNF295-AS1	ENST00000676087.2		n.432+7539T>C		intron	N/A
	ZNF295-AS1	ENST00000676145.1		n.72-2454T>C		intron	N/A

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

African (AFR) AF: 0.258 AC: 10704 AN: 41460

American (AMR) AF: 0.776 AC: 11867 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.596 AC: 3079 AN: 5166

South Asian (SAS) AF: 0.771 AC: 3714 AN: 4816

European-Finnish (FIN) AF: 0.851 AC: 9012 AN: 10594

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55257 AN: 68002

Other (OTH) AF: 0.674 AC: 1420 AN: 2106

Alfa AF: 0.763 Hom.: 131553

Bravo AF: 0.627

Asia WGS AF: 0.636 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs220245;

hg19: chr21-43459172;