rs2341629

Positions:

• chrX-71231039-G-A
• chrX-71231039-G-C

Variant summary

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

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 0.59 (14516 hom., 18754 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71231039G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 64887 AN: 109744 Hom.: 14504 Cov.: 22 AF XY: 0.584 AC XY: 18697 AN XY: 32028

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.616

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: 0.592 AC: 64956 AN: 109800 Hom.: 14516 Cov.: 22 AF XY: 0.584 AC XY: 18754 AN XY: 32094

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.622

Alfa AF: 0.520 Hom.: 35079

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2341629; hg19: chrX-70450889;