X-43391471-G-A

Variant names:

• chrX-43391471-G-A
• rs1155699
• ENST00000649774.1:n.227-3814G>A

Variant summary

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

The ENST00000649774.1(ENSG00000285899):​n.227-3814G>A 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 0.60 (14153 hom., 19192 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000285899 ENST00000649774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 3 publications found

Genes affected

ENSG00000285899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649774.1. 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
	ENSG00000285899	ENST00000649774.1		n.227-3814G>A		intron	N/A
	ENSG00000285899	ENST00000811237.1		n.298-46864G>A		intron	N/A
	ENSG00000285899	ENST00000811238.1		n.253-3814G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 65719 AN: 110176 Hom.: 14155 Cov.: 22

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.600

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: 0.597 AC: 65755 AN: 110228 Hom.: 14153 Cov.: 22 AF XY: 0.590 AC XY: 19192 AN XY: 32534

African (AFR) AF: 0.498 AC: 15095 AN: 30321

American (AMR) AF: 0.702 AC: 7281 AN: 10365

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1463 AN: 2629

East Asian (EAS) AF: 0.595 AC: 2067 AN: 3476

South Asian (SAS) AF: 0.455 AC: 1185 AN: 2606

European-Finnish (FIN) AF: 0.615 AC: 3548 AN: 5771

Middle Eastern (MID) AF: 0.629 AC: 132 AN: 210

European-Non Finnish (NFE) AF: 0.640 AC: 33715 AN: 52665

Other (OTH) AF: 0.600 AC: 906 AN: 1511

Alfa AF: 0.625 Hom.: 7540

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.89
DANN	Benign	0.43
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1155699; hg19: chrX-43250720;