chrX-8328098-G-A

Variant names:

• chrX-8328098-G-A
• rs1921708
• ENST00000659022.1:n.1043-41466G>A

Variant summary

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

The ENST00000659022.1(ENSG00000285679):​n.1043-41466G>A variant causes a intron 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 0.61 (15868 hom., 19886 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000285679 ENST00000659022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 4 publications found

Genes affected

ENSG00000285679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659022.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285679	ENST00000659022.1		n.1043-41466G>A		intron	N/A
	ENSG00000285679	ENST00000746116.1		n.72-92989G>A		intron	N/A
	ENSG00000285679	ENST00000746117.1		n.72-97179G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 67652 AN: 110401 Hom.: 15856 Cov.: 23

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.635

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: 0.613 AC: 67725 AN: 110455 Hom.: 15868 Cov.: 23 AF XY: 0.608 AC XY: 19886 AN XY: 32713

African (AFR) AF: 0.862 AC: 26203 AN: 30400

American (AMR) AF: 0.642 AC: 6647 AN: 10355

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1276 AN: 2630

East Asian (EAS) AF: 0.789 AC: 2723 AN: 3453

South Asian (SAS) AF: 0.536 AC: 1394 AN: 2602

European-Finnish (FIN) AF: 0.402 AC: 2335 AN: 5810

Middle Eastern (MID) AF: 0.596 AC: 127 AN: 213

European-Non Finnish (NFE) AF: 0.487 AC: 25726 AN: 52817

Other (OTH) AF: 0.638 AC: 960 AN: 1504

Alfa AF: 0.547 Hom.: 19870

Bravo AF: 0.648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.47
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1921708; hg19: chrX-8296139;