rs732214

chr12-69422046-T-C

Variant summary

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

The XR_944742.4(YEATS4):n.860-1955T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,750 control chromosomes in the GnomAD database, including 11,063 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 (11063 hom., cov: 31)
• Consequence: YEATS4 XR_944742.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

YEATS4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YEATS4	XR_007063127.1	n.859+14772T>C		intron_variant, non_coding_transcript_variant
YEATS4	XR_007063131.1	n.859+14772T>C		intron_variant, non_coding_transcript_variant
YEATS4	XR_944742.4	n.860-1955T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56690 AN: 151632 Hom.: 11054 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.374 AC: 56740 AN: 151750 Hom.: 11063 Cov.: 31 AF XY: 0.379 AC XY: 28079 AN XY: 74150

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.357

Alfa AF: 0.326 Hom.: 10994

Bravo AF: 0.372

Asia WGS AF: 0.536 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
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: rs732214; hg19: chr12-69815826;