rs2834036

chr21-32971825-T-C

Variant summary

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

The ENST00000454622.2(ENSG00000227757):n.202-57696A>G 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 0.444 in 151,872 control chromosomes in the GnomAD database, including 16,991 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 0.44 (16991 hom., cov: 31)
• Consequence: ENST00000454622.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

Genes affected

(HGNC:):

C21orf62-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000454622.2	n.202-57696A>G		intron_variant, non_coding_transcript_variant		2
C21orf62-AS1	ENST00000700822.1	n.487-47559T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67338 AN: 151750 Hom.: 16965 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.444 AC: 67403 AN: 151872 Hom.: 16991 Cov.: 31 AF XY: 0.435 AC XY: 32299 AN XY: 74224

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.0697

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.414

Alfa AF: 0.378 Hom.: 16464

Bravo AF: 0.458

Asia WGS AF: 0.210 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.88
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834036; hg19: chr21-34344133;