rs1573704

Positions:

• chrX-129125504-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000660383.1(ENSG00000225689):​n.144+2760A>C 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 0.68 (18015 hom., 21775 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENST00000660383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905213	XR_007068324.1	n.1012-3311A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660383.1	n.144+2760A>C		intron_variant, non_coding_transcript_variant
	ENST00000653849.1	n.1101-3311A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.675 AC: 74415 AN: 110170 Hom.: 18005 Cov.: 23 AF XY: 0.670 AC XY: 21734 AN XY: 32424

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.733

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.713

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: 0.676 AC: 74463 AN: 110226 Hom.: 18015 Cov.: 23 AF XY: 0.670 AC XY: 21775 AN XY: 32490

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.717

Alfa AF: 0.705 Hom.: 28271

Bravo AF: 0.686

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1573704; hg19: chrX-128259481;