rs4817502

Positions:

• chr21-32802930-C-G
• chrNW_003315969.2-33852-C-G
• chr21-32802930-C-A
• chrNW_003315969.2-33852-C-A
• chr21-32802930-C-T
• chrNW_003315969.2-33852-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001162495.3(C21orf62):​c.-65+4712G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.72

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;