rs1921708

chrX-8328098-G-AchrX-8328098-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000659022.1(ENSG00000285679):n.1043-41466G>A variant causes a intron, non coding transcript 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: ENST00000659022.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS2: High Homozygotes in GnomAd at 15856 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985675	XR_001755783.2	n.1986-92989G>A		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755782.2	n.1985+99693G>A		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755784.2	n.1985+99693G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659022.1	n.1043-41466G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.613 AC: 67652 AN: 110401 Hom.: 15856 Cov.: 23 AF XY: 0.607 AC XY: 19826 AN XY: 32649

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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.638

Alfa AF: 0.526 Hom.: 12221

Bravo AF: 0.648

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.54
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921708; hg19: chrX-8296139;