X-12892402-A-G

Variant names:

• chrX-12892402-A-G
• rs179006
• ENST00000827469.1:n.1107T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000827469.1(ENSG00000307619):​n.1107T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.82 (26120 hom., 26767 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000307619 ENST00000827469.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 8 publications found

Genes affected

ENSG00000307619 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827469.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307619	ENST00000827469.1		n.1107T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.820 AC: 90325 AN: 110087 Hom.: 26116 Cov.: 22

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.808

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.821 AC: 90386 AN: 110144 Hom.: 26120 Cov.: 22 AF XY: 0.827 AC XY: 26767 AN XY: 32368

African (AFR) AF: 0.836 AC: 25274 AN: 30235

American (AMR) AF: 0.863 AC: 8873 AN: 10284

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 1947 AN: 2627

East Asian (EAS) AF: 1.00 AC: 3517 AN: 3518

South Asian (SAS) AF: 0.921 AC: 2379 AN: 2582

European-Finnish (FIN) AF: 0.860 AC: 4968 AN: 5778

Middle Eastern (MID) AF: 0.781 AC: 168 AN: 215

European-Non Finnish (NFE) AF: 0.789 AC: 41632 AN: 52747

Other (OTH) AF: 0.810 AC: 1203 AN: 1485

Alfa AF: 0.801 Hom.: 85384

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs179006; hg19: chrX-12910521;