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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288098	ENST00000664519.1		n.442+2384A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6529006;

hg19: chrX-141473295;