rs117124364

chr21-32997453-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000454622.2(ENSG00000227757):n.201+73451G>A 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 0.0102 in 152,268 control chromosomes in the GnomAD database, including 3 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 0.010 (3 hom., cov: 32)
• Consequence: ENST00000454622.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0102 (1548/152268) while in subpopulation NFE AF= 0.0164 (1114/68030). AF 95% confidence interval is 0.0156. There are 3 homozygotes in gnomad4. There are 691 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 3 gene

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.201+73451G>A		intron_variant, non_coding_transcript_variant		2
C21orf62-AS1	ENST00000700822.1	n.487-21931C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1549 AN: 152150 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00345

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.00989

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.00861

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

GnomAD4 genome AF: 0.0102 AC: 1548 AN: 152268 Hom.: 3 Cov.: 32 AF XY: 0.00928 AC XY: 691 AN XY: 74450

Gnomad4 AFR AF: 0.00344

Gnomad4 AMR AF: 0.00987

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.00852

Alfa AF: 0.0125 Hom.: 0

Bravo AF: 0.0109

Asia WGS AF: 0.00289 AC: 10 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	1.4
Dann	Benign	0.084

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117124364; hg19: chr21-34369761;