21-36130724-C-T

Position:

• chr21-36130724-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEMO1P1	ENST00000452572.1	n.236C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.745

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.785

Gnomad4 EAS exome AF: 0.845

Gnomad4 SAS exome AF: 0.789

Gnomad4 FIN exome AF: 0.730

Gnomad4 NFE exome AF: 0.817

Gnomad4 OTH exome AF: 0.804

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

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.794

Alfa AF: 0.801 Hom.: 15980

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2242802; hg19: chr21-37503022;