chr21-32802930-C-A

Position:

• chr21-32802930-C-A

Variant summary

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

The NM_001162495.3(C21orf62):​c.-65+4712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,048 control chromosomes in the GnomAD database, including 39,904 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 0.72 (39904 hom., cov: 31)
• Consequence: C21orf62 NM_001162495.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C21orf62	NM_001162495.3	c.-65+4712G>T		intron_variant		ENST00000479548.2	NP_001155967.2
C21orf62	NM_001162496.3	c.-64-8445G>T		intron_variant			NP_001155968.2
C21orf62	NM_019596.6	c.-65+7644G>T		intron_variant			NP_062542.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C21orf62	ENST00000479548.2	c.-65+4712G>T		intron_variant		1	NM_001162495.3	ENSP00000418653	P1
C21orf62-AS1	ENST00000700822.1	n.294+18011C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108926 AN: 151930 Hom.: 39887 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.717 AC: 108993 AN: 152048 Hom.: 39904 Cov.: 31 AF XY: 0.721 AC XY: 53564 AN XY: 74332

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.681

Alfa AF: 0.746 Hom.: 19135

Bravo AF: 0.708

Asia WGS AF: 0.749 AC: 2606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.81

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: rs4817502; hg19: chr21-34175240;