chr21-42045938-T-C

Position:

• chr21-42045938-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.233-7961T>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 0.238 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 ENST00000676087.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

Genes affected

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

LOC107985502 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107985502	XR_001755063.3	n.1324+3956T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF295-AS1	ENST00000676087.1	n.233-7961T>C		intron_variant, non_coding_transcript_variant
ZNF295-AS1	ENST00000669320.1	n.324-7961T>C		intron_variant, non_coding_transcript_variant
ZNF295-AS1	ENST00000676145.1	n.537+3956T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0511

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.236

Alfa AF: 0.260 Hom.: 10279

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2839452; hg19: chr21-43466047;