NM_005748.6:c.152+1701G>A

Variant names:

• chr12-42235898-C-T
• rs529702417
• NM_005748.6:c.152+1701G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Moderate BP6_Moderate BS2

The NM_005748.6(YAF2):​c.152+1701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000393 in 1,536,116 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00042 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00039 (2 hom.)
• Consequence: YAF2 NM_005748.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.95
• Publications: 1 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BP6: Variant 12-42235898-C-T is Benign according to our data. Variant chr12-42235898-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2642901.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 64 AD gene.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YAF2	NM_005748.6	MANE Select	c.152+1701G>A		intron	N/A	NP_005739.2	Q8IY57-1
	YAF2	NM_001190980.3		c.252G>A	p.Glu84Glu	synonymous	Exon 3 of 3	NP_001177909.1	Q8IY57-4
	YAF2	NM_001190979.3		c.152+1701G>A		intron	N/A	NP_001177908.1	Q8IY57-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YAF2	ENST00000534854.7	TSL:1 MANE Select	c.152+1701G>A		intron	N/A	ENSP00000439256.2	Q8IY57-1
	YAF2	ENST00000327791.8	TSL:1	c.152+1701G>A		intron	N/A	ENSP00000328004.5	Q8IY57-5
	YAF2	ENST00000555248.2	TSL:2	c.252G>A	p.Glu84Glu	synonymous	Exon 3 of 3	ENSP00000451626.2	Q8IY57-4

Frequencies

GnomAD3 genomes AF: 0.000421 AC: 64 AN: 152164 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000590

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000470

Gnomad OTH AF: 0.000956

GnomAD2 exomes AF: 0.000713 AC: 96 AN: 134600 AF XY: 0.000696

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000449

Gnomad ASJ exome AF: 0.00458

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000186

Gnomad NFE exome AF: 0.000530

Gnomad OTH exome AF: 0.000724

GnomAD4 exome AF: 0.000390 AC: 540 AN: 1383834 Hom.: 2 Cov.: 34 AF XY: 0.000401 AC XY: 274 AN XY: 682858

African (AFR) AF: 0.0000317 AC: 1 AN: 31594

American (AMR) AF: 0.000364 AC: 13 AN: 35700

Ashkenazi Jewish (ASJ) AF: 0.00377 AC: 95 AN: 25182

East Asian (EAS) AF: 0.00 AC: 0 AN: 35734

South Asian (SAS) AF: 0.000833 AC: 66 AN: 79236

European-Finnish (FIN) AF: 0.0000885 AC: 3 AN: 33900

Middle Eastern (MID) AF: 0.000702 AC: 4 AN: 5696

European-Non Finnish (NFE) AF: 0.000294 AC: 317 AN: 1078884

Other (OTH) AF: 0.000708 AC: 41 AN: 57908

GnomAD4 genome AF: 0.000420 AC: 64 AN: 152282 Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32 AN XY: 74458

African (AFR) AF: 0.0000722 AC: 3 AN: 41552

American (AMR) AF: 0.000589 AC: 9 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000470 AC: 32 AN: 68024

Other (OTH) AF: 0.000946 AC: 2 AN: 2114

Alfa AF: 0.00104 Hom.: 0

Bravo AF: 0.000404

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	20
DANN	Benign	0.66
PhyloP100		2.9
Mutation Taster		=100/0	polymorphism

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: rs529702417; hg19: chr12-42629700;