rs17813347

Variant names:

• chr12-69416372-G-T
• rs17813347
• XR_944742.4:n.860-7629G>T

Variant summary

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

The XR_944742.4(YEATS4):​n.860-7629G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,288 control chromosomes in the GnomAD database, including 191 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 0.042 (191 hom., cov: 32)
• Consequence: YEATS4 XR_944742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

Genes affected

YEATS4 (HGNC:24859): (YEATS domain containing 4) The protein encoded by this gene is found in the nucleoli. It has high sequence homology to human MLLT1, and yeast and human MLLT3 proteins. Both MLLT1 and MLLT3 proteins belong to a class of transcription factors, indicating that the encoded protein might also represent a transcription factor. This protein is thought to be required for RNA transcription. This gene has been shown to be amplified in tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YEATS4	XR_944742.4	n.860-7629G>T		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0417 AC: 6346 AN: 152170 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0417 AC: 6344 AN: 152288 Hom.: 191 Cov.: 32 AF XY: 0.0398 AC XY: 2963 AN XY: 74466

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0426

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0619 Hom.: 313

Bravo AF: 0.0416

Asia WGS AF: 0.00751 AC: 26 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17813347; hg19: chr12-69810152;