rs2242802

Variant names:

• chr21-36130724-C-A
• rs2242802
• ENST00000452572.1:n.236C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-36130724-C-A
• chr21-36130724-C-G
• chr21-36130724-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000452572.1(MEMO1P1):​n.236C>A variant causes a non coding transcript exon change. 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: 32)
• Consequence: MEMO1P1 ENST00000452572.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.66
• Publications: 7 publications found

Genes affected

MEMO1P1 (HGNC:23274): (MEMO1 pseudogene 1)

CBR3-AS1 (HGNC:43664): (CBR3 antisense RNA 1)

ENSG00000295944 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEMO1P1		n.36130724C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEMO1P1	ENST00000452572.1	n.236C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
CBR3-AS1	ENST00000733836.1	n.1203G>T		non_coding_transcript_exon_variant	Exon 1 of 2
CBR3-AS1	ENST00000733837.1	n.299G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 66

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	8.2
DANN	Benign	0.92
PhyloP100		5.7

Splicing

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

Other links and lift over

dbSNP: rs2242802; hg19: chr21-37503022;