chr12-42226575-G-A

Variant names:

• chr12-42226575-G-A
• rs10785334
• NM_005748.6:c.152+11024C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005748.6. 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
	YAF2	NM_005748.6	MANE Select	c.152+11024C>T		intron	N/A	NP_005739.2
	YAF2	NM_001190979.3		c.152+11024C>T		intron	N/A	NP_001177908.1
	YAF2	NM_001320080.2		c.25+11024C>T		intron	N/A	NP_001307009.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YAF2	ENST00000534854.7	TSL:1 MANE Select	c.152+11024C>T		intron	N/A	ENSP00000439256.2
	YAF2	ENST00000327791.8	TSL:1	c.152+11024C>T		intron	N/A	ENSP00000328004.5
	YAF2	ENST00000380790.4	TSL:2	c.26+11580C>T		intron	N/A	ENSP00000370167.4

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

African (AFR) AF: 0.338 AC: 13982 AN: 41418

American (AMR) AF: 0.315 AC: 4805 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2138 AN: 5150

South Asian (SAS) AF: 0.483 AC: 2322 AN: 4812

European-Finnish (FIN) AF: 0.445 AC: 4672 AN: 10510

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25893 AN: 67958

Other (OTH) AF: 0.351 AC: 738 AN: 2104

Alfa AF: 0.267 Hom.: 905

Bravo AF: 0.355

Asia WGS AF: 0.427 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.095
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10785334; hg19: chr12-42620377;