rs6529006

Variant names:

• chrX-142385509-A-G
• rs6529006
• ENST00000664519.1:n.442+2384A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-142385509-A-G
• chrX-142385509-A-T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.442+2384A>G variant causes a intron 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: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925
• Publications: 0 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288098	ENST00000664519.1	n.442+2384A>G		intron_variant	Intron 4 of 9

Frequencies

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

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

African (AFR) AF: 0.914 AC: 27534 AN: 30120

American (AMR) AF: 0.933 AC: 9556 AN: 10246

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 2611 AN: 2633

East Asian (EAS) AF: 0.848 AC: 2880 AN: 3398

South Asian (SAS) AF: 0.958 AC: 2372 AN: 2475

European-Finnish (FIN) AF: 0.995 AC: 5577 AN: 5605

Middle Eastern (MID) AF: 0.967 AC: 208 AN: 215

European-Non Finnish (NFE) AF: 0.988 AC: 52079 AN: 52735

Other (OTH) AF: 0.964 AC: 1439 AN: 1492

Alfa AF: 0.972 Hom.: 79756

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6529006; hg19: chrX-141473295;