rs73351675

Positions:

• chr17-50508193-T-C
• chr17-50508193-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047436908.1(MYCBPAP):​c.142+93T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 238,362 control chromosomes in the GnomAD database, including 35,388 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 0.55 (25935 hom., cov: 32)
  • Exomes 𝑓: 0.46 (9453 hom.)
• Consequence: MYCBPAP XM_047436908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

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

ENSG00000249451 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYCBPAP	XM_047436908.1	c.142+93T>C		intron_variant			XP_047292864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249451	ENST00000502300.1	n.27+109A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83870 AN: 151934 Hom.: 25864 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.503

GnomAD4 exome AF: 0.458 AC: 39504 AN: 86310 Hom.: 9453 AF XY: 0.459 AC XY: 20547 AN XY: 44748

Gnomad4 AFR exome AF: 0.861

Gnomad4 AMR exome AF: 0.576

Gnomad4 ASJ exome AF: 0.559

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.461

Gnomad4 NFE exome AF: 0.447

Gnomad4 OTH exome AF: 0.480

GnomAD4 genome AF: 0.552 AC: 84008 AN: 152052 Hom.: 25935 Cov.: 32 AF XY: 0.548 AC XY: 40724 AN XY: 74362

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.509

Alfa AF: 0.502 Hom.: 2605

Bravo AF: 0.574

Asia WGS AF: 0.372 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73351675; hg19: chr17-48585554;