17-50513848-A-G

Position:

• chr17-50513848-A-G

Variant summary

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

The NM_032133.6(MYCBPAP):​c.77-2722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,058 control chromosomes in the GnomAD database, including 11,854 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 0.35 (11854 hom., cov: 32)
• Consequence: MYCBPAP NM_032133.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

Genes affected

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

MYCBPAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYCBPAP	NM_032133.6	c.77-2722A>G		intron_variant		ENST00000323776.11	NP_115509.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYCBPAP	ENST00000323776.11	c.77-2722A>G		intron_variant		1	NM_032133.6	ENSP00000323184.6

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52452 AN: 151936 Hom.: 11810 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.346 AC: 52561 AN: 152058 Hom.: 11854 Cov.: 32 AF XY: 0.341 AC XY: 25359 AN XY: 74348

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.324

Alfa AF: 0.228 Hom.: 3731

Bravo AF: 0.377

Asia WGS AF: 0.221 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.6
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6504663; hg19: chr17-48591209;