rs2766692

Variant names:

• chr14-100217855-A-G
• rs2766692
• ENST00000554537.2:n.135-10203T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-100217855-A-G
• chr14-100217855-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554537.2(YY1-DT):​n.135-10203T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,102 control chromosomes in the GnomAD database, including 38,049 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 0.71 (38049 hom., cov: 32)
• Consequence: YY1-DT ENST00000554537.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 17 publications found

Genes affected

YY1-DT (HGNC:56936):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YY1-DT	NR_189150.1	n.152-10203T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YY1-DT	ENST00000554537.2	n.135-10203T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107217 AN: 151984 Hom.: 38004 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.706 AC: 107320 AN: 152102 Hom.: 38049 Cov.: 32 AF XY: 0.701 AC XY: 52156 AN XY: 74366

African (AFR) AF: 0.748 AC: 31040 AN: 41490

American (AMR) AF: 0.644 AC: 9832 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2602 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3210 AN: 5180

South Asian (SAS) AF: 0.468 AC: 2255 AN: 4820

European-Finnish (FIN) AF: 0.734 AC: 7772 AN: 10590

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48286 AN: 67970

Other (OTH) AF: 0.705 AC: 1490 AN: 2112

Alfa AF: 0.702 Hom.: 125020

Bravo AF: 0.705

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.46
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2766692; hg19: chr14-100684192;