ENST00000502300.1:n.27+109A>T

Variant names:

• chr17-50508193-T-A
• rs73351675
• ENST00000502300.1:n.27+109A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000502300.1(ENSG00000249451):​n.27+109A>T 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000249451 ENST00000502300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 0 publications found

Genes affected

ENSG00000249451 (HGNC:):

MYCBPAP (HGNC:19677): (MYCBP associated protein) Involved in spermatogenesis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYCBPAP Gene-Disease associations (from GenCC):

• spermatogenic failure

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502300.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCBPAP	NM_032133.6	MANE Select	c.-482T>A		upstream_gene	N/A	NP_115509.5
	MYCBPAP	NM_001366294.2		c.-482T>A		upstream_gene	N/A	NP_001353223.1
	MYCBPAP	NR_158785.2		n.-246T>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249451	ENST00000502300.1	TSL:5	n.27+109A>T		intron	N/A
	MYCBPAP	ENST00000323776.11	TSL:1 MANE Select	c.-482T>A		upstream_gene	N/A	ENSP00000323184.6
	MYCBPAP	ENST00000470609.5	TSL:5	n.-232T>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 86556 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 44870

African (AFR) AF: 0.00 AC: 0 AN: 1510

American (AMR) AF: 0.00 AC: 0 AN: 1032

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2660

East Asian (EAS) AF: 0.00 AC: 0 AN: 2648

South Asian (SAS) AF: 0.00 AC: 0 AN: 10070

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5754

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 428

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 56830

Other (OTH) AF: 0.00 AC: 0 AN: 5624

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-1.4
PromoterAI		0.42	Neutral

Splicing

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

Other links and lift over

dbSNP: rs73351675; hg19: chr17-48585554;