X-12892500-T-G

Variant names:

• chrX-12892500-T-G
• rs2269809
• ENST00000827469.1:n.1009A>C

Variant summary

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

The ENST00000827469.1(ENSG00000307619):​n.1009A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 110,839 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 13,586 hemizygotes in GnomAD. 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 0.43 (7652 hom., 13586 hem., cov: 23)
• Consequence: ENSG00000307619 ENST00000827469.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 2 publications found

Genes affected

ENSG00000307619 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307619	ENST00000827469.1	n.1009A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 47840 AN: 110785 Hom.: 7652 Cov.: 23

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.432 AC: 47864 AN: 110839 Hom.: 7652 Cov.: 23 AF XY: 0.411 AC XY: 13586 AN XY: 33093

African (AFR) AF: 0.449 AC: 13669 AN: 30410

American (AMR) AF: 0.362 AC: 3784 AN: 10439

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 863 AN: 2633

East Asian (EAS) AF: 0.176 AC: 627 AN: 3570

South Asian (SAS) AF: 0.356 AC: 949 AN: 2665

European-Finnish (FIN) AF: 0.416 AC: 2448 AN: 5881

Middle Eastern (MID) AF: 0.421 AC: 91 AN: 216

European-Non Finnish (NFE) AF: 0.465 AC: 24565 AN: 52837

Other (OTH) AF: 0.417 AC: 632 AN: 1515

Alfa AF: 0.441 Hom.: 29562

Bravo AF: 0.428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.99
DANN	Benign	0.71
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2269809; hg19: chrX-12910619;