rs1337082

chrX-67764173-G-AchrX-67764173-G-C

Variant summary

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

The XR_938423.3(NXTAR):n.82-2207C>T 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 0.63 (18384 hom., 21525 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: NXTAR XR_938423.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

NXTAR (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 18392 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NXTAR	XR_938423.3	n.82-2207C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.627 AC: 69698 AN: 111141 Hom.: 18392 Cov.: 24 AF XY: 0.645 AC XY: 21509 AN XY: 33341

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.661

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: 0.627 AC: 69690 AN: 111197 Hom.: 18384 Cov.: 24 AF XY: 0.644 AC XY: 21525 AN XY: 33407

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.665

Alfa AF: 0.744 Hom.: 11229

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.9
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1337082; hg19: chrX-66984015;