rs10785334

chr12-42226575-G-Achr12-42226575-G-T

Variant summary

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

The NM_005748.6(YAF2):c.152+11024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,880 control chromosomes in the GnomAD database, including 10,611 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 0.37 (10611 hom., cov: 31)
• Consequence: YAF2 NM_005748.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

YAF2 (HGNC:17363): (YY1 associated factor 2) This gene encodes a zinc finger containing protein that functions in the regulation of transcription. This protein was identified as an interacting partner of transcriptional repressor protein Yy1, and also interacts with other transcriptional regulators, including Myc and Polycomb. This protein can promote proteolysis of Yy1. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YAF2	NM_005748.6	c.152+11024C>T		intron_variant		ENST00000534854.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YAF2	ENST00000534854.7	c.152+11024C>T		intron_variant		1	NM_005748.6	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56261 AN: 151760 Hom.: 10602 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.371 AC: 56309 AN: 151880 Hom.: 10611 Cov.: 31 AF XY: 0.377 AC XY: 27997 AN XY: 74222

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.351

Alfa AF: 0.264 Hom.: 863

Bravo AF: 0.355

Asia WGS AF: 0.427 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.095

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: rs10785334; hg19: chr12-42620377;