rs179007

Variant names:

• chrX-12892203-G-A
• rs179007
• ENST00000827469.1:n.1306C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-12892203-G-A
• chrX-12892203-G-C

Variant summary

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

The ENST00000827469.1(ENSG00000307619):​n.1306C>T 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 0.81 (25371 hom., 23673 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000307619 ENST00000827469.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 9 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307619	ENST00000827469.1		n.1306C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.806 AC: 86210 AN: 106898 Hom.: 25365 Cov.: 20

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.796

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: 0.807 AC: 86259 AN: 106940 Hom.: 25371 Cov.: 20 AF XY: 0.807 AC XY: 23673 AN XY: 29346

African (AFR) AF: 0.842 AC: 24644 AN: 29279

American (AMR) AF: 0.852 AC: 8382 AN: 9837

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 1908 AN: 2591

East Asian (EAS) AF: 1.00 AC: 3432 AN: 3433

South Asian (SAS) AF: 0.913 AC: 2147 AN: 2352

European-Finnish (FIN) AF: 0.805 AC: 4212 AN: 5234

Middle Eastern (MID) AF: 0.776 AC: 166 AN: 214

European-Non Finnish (NFE) AF: 0.767 AC: 39836 AN: 51913

Other (OTH) AF: 0.799 AC: 1139 AN: 1426

Alfa AF: 0.793 Hom.: 52403

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.042
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs179007;

hg19: chrX-12910322;