rs6529006

chrX-142385509-A-GchrX-142385509-A-T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):n.442+2384A>G 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 0.96 (35708 hom., 30467 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd at 35707 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664519.1	n.442+2384A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.957 AC: 104894 AN: 109567 Hom.: 35707 Cov.: 22 AF XY: 0.957 AC XY: 30421 AN XY: 31793

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.963

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: 0.957 AC: 104935 AN: 109606 Hom.: 35708 Cov.: 22 AF XY: 0.957 AC XY: 30467 AN XY: 31842

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.964

Alfa AF: 0.981 Hom.: 52719

Bravo AF: 0.950

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.12
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6529006; hg19: chrX-141473295;