chr21-36130724-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000452572.1(MEMO1P1):​n.236C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.805 in 1,610,608 control chromosomes in the GnomAD database, including 523,507 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 0.78 (46278 hom., cov: 32)
  • Exomes 𝑓: 0.81 (477229 hom.)
• 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118509 AN: 152070 Hom.: 46247 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.797

GnomAD4 exome AF: 0.808 AC: 1178718 AN: 1458420 Hom.: 477229 Cov.: 66 AF XY: 0.808 AC XY: 586393 AN XY: 725582

African (AFR) AF: 0.745 AC: 24878 AN: 33394

American (AMR) AF: 0.750 AC: 33525 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 20492 AN: 26092

East Asian (EAS) AF: 0.845 AC: 33536 AN: 39698

South Asian (SAS) AF: 0.789 AC: 67953 AN: 86158

European-Finnish (FIN) AF: 0.730 AC: 38942 AN: 53314

Middle Eastern (MID) AF: 0.811 AC: 3369 AN: 4156

European-Non Finnish (NFE) AF: 0.817 AC: 907651 AN: 1110720

Other (OTH) AF: 0.804 AC: 48372 AN: 60174

GnomAD4 genome AF: 0.779 AC: 118591 AN: 152188 Hom.: 46278 Cov.: 32 AF XY: 0.775 AC XY: 57678 AN XY: 74406

African (AFR) AF: 0.737 AC: 30582 AN: 41518

American (AMR) AF: 0.769 AC: 11756 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2713 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4376 AN: 5184

South Asian (SAS) AF: 0.797 AC: 3844 AN: 4824

European-Finnish (FIN) AF: 0.733 AC: 7748 AN: 10574

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55010 AN: 68024

Other (OTH) AF: 0.794 AC: 1679 AN: 2114

Alfa AF: 0.802 Hom.: 18469

Bravo AF: 0.783

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	8.8
DANN	Benign	0.93
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;