rs11177669

Positions:

• chr12-69434901-G-A
• chr12-69434901-G-C

Variant summary

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

The XR_007063127.1(YEATS4):​n.860-24616G>A 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 0.277 in 152,080 control chromosomes in the GnomAD database, including 5,911 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 0.28 (5911 hom., cov: 32)
• Consequence: YEATS4 XR_007063127.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

YEATS4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
YEATS4	XR_007063127.1	n.860-24616G>A		intron_variant, non_coding_transcript_variant
YEATS4	XR_007063131.1	n.860-24616G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42061 AN: 151962 Hom.: 5890 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.277 AC: 42137 AN: 152080 Hom.: 5911 Cov.: 32 AF XY: 0.277 AC XY: 20568 AN XY: 74338

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.272

Alfa AF: 0.259 Hom.: 11214

Bravo AF: 0.276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11177669; hg19: chr12-69828681;