chrX-46760260-A-G

Variant names:

• chrX-46760260-A-G
• rs3810662
• ENST00000818472.1:n.176+1458A>G

Variant summary

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

The ENST00000818472.1(ENSG00000306433):​n.176+1458A>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 0.61 (16265 hom., 20093 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000306433 ENST00000818472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 publications found

Genes affected

ENSG00000306433 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818472.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306433	ENST00000818472.1		n.176+1458A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 67955 AN: 110834 Hom.: 16256 Cov.: 23

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.604

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: 0.613 AC: 68017 AN: 110888 Hom.: 16265 Cov.: 23 AF XY: 0.607 AC XY: 20093 AN XY: 33100

African (AFR) AF: 0.899 AC: 27392 AN: 30459

American (AMR) AF: 0.584 AC: 6127 AN: 10496

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1310 AN: 2632

East Asian (EAS) AF: 0.842 AC: 2961 AN: 3515

South Asian (SAS) AF: 0.683 AC: 1804 AN: 2641

European-Finnish (FIN) AF: 0.431 AC: 2541 AN: 5889

Middle Eastern (MID) AF: 0.606 AC: 131 AN: 216

European-Non Finnish (NFE) AF: 0.464 AC: 24499 AN: 52846

Other (OTH) AF: 0.610 AC: 928 AN: 1521

Alfa AF: 0.542 Hom.: 54429

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3810662; hg19: chrX-46619695;