rs3810662

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-46760260-A-G
• chrX-46760260-A-T

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).

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
ENSG00000306433	ENST00000818472.1	n.176+1458A>G		intron_variant	Intron 1 of 1

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 v4.3

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;