21-32796263-G-A

Position:

• chr21-32796263-G-A

Variant summary

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

The NM_001162495.3(C21orf62):​c.-64-1778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,234 control chromosomes in the GnomAD database, including 987 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 0.11 (987 hom., cov: 32)
• Consequence: C21orf62 NM_001162495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

Genes affected

C21orf62 (HGNC:1305): (exosomal polycystin 1 interacting protein)

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C21orf62	NM_001162495.3	c.-64-1778C>T		intron_variant		ENST00000479548.2
C21orf62-AS1	NR_024622.1	n.435-676G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C21orf62	ENST00000479548.2	c.-64-1778C>T		intron_variant		1	NM_001162495.3	P1
C21orf62-AS1	ENST00000700822.1	n.294+11344G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16500 AN: 152114 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.109 AC: 16521 AN: 152234 Hom.: 987 Cov.: 32 AF XY: 0.108 AC XY: 8009 AN XY: 74438

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0792

Gnomad4 EAS AF: 0.00831

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0973 Hom.: 778

Bravo AF: 0.109

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2154427; hg19: chr21-34168573;