rs1573704

Variant names:

• chrX-129125504-T-G
• rs1573704
• XR_007068316.1:n.1760A>C

Variant summary

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

The XR_007068316.1(LOC124905213):​n.1760A>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 0.68 (18015 hom., 21775 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LOC124905213 XR_007068316.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 1 publications found

Genes affected

LOC124905213 (HGNC:):

ACMG classification

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905213	XR_007068316.1	n.1760A>C		non_coding_transcript_exon_variant	Exon 1 of 7
LOC124905213	XR_007068317.1	n.1760A>C		non_coding_transcript_exon_variant	Exon 1 of 6
LOC124905213	XR_007068318.1	n.1760A>C		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225689	ENST00000653849.1	n.1101-3311A>C		intron_variant	Intron 3 of 6
ENSG00000225689	ENST00000660383.1	n.144+2760A>C		intron_variant	Intron 1 of 10
ENSG00000301792	ENST00000781917.1	n.49-24635T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.675 AC: 74415 AN: 110170 Hom.: 18005 Cov.: 23

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

African (AFR) AF: 0.597 AC: 18060 AN: 30268

American (AMR) AF: 0.775 AC: 7983 AN: 10307

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1779 AN: 2626

East Asian (EAS) AF: 0.600 AC: 2086 AN: 3476

South Asian (SAS) AF: 0.763 AC: 1973 AN: 2585

European-Finnish (FIN) AF: 0.622 AC: 3634 AN: 5839

Middle Eastern (MID) AF: 0.744 AC: 157 AN: 211

European-Non Finnish (NFE) AF: 0.705 AC: 37161 AN: 52735

Other (OTH) AF: 0.717 AC: 1076 AN: 1501

Alfa AF: 0.701 Hom.: 40440

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
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1573704; hg19: chrX-128259481;