12-69433878-G-T

Position:

• chr12-69433878-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007063127.1(YEATS4):​n.860-25639G>T 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 0.424 in 152,010 control chromosomes in the GnomAD database, including 14,555 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 0.42 (14555 hom., cov: 32)
• Consequence: YEATS4 XR_007063127.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

YEATS4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YEATS4	XR_007063127.1	n.860-25639G>T		intron_variant, non_coding_transcript_variant
YEATS4	XR_007063131.1	n.860-25639G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64304 AN: 151892 Hom.: 14525 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.424 AC: 64393 AN: 152010 Hom.: 14555 Cov.: 32 AF XY: 0.424 AC XY: 31513 AN XY: 74300

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.398

Alfa AF: 0.356 Hom.: 22458

Bravo AF: 0.426

Asia WGS AF: 0.583 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10748128; hg19: chr12-69827658;