rs223686

Variant names:

• chrX-89503121-G-T
• rs223686
• ENST00000798091.1:n.222-402C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000798091.1(ENSG00000303925):​n.222-402C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 109,599 control chromosomes in the GnomAD database, including 3,975 homozygotes. There are 9,100 hemizygotes in GnomAD. 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 0.29 (3975 hom., 9100 hem., cov: 21)
• Consequence: ENSG00000303925 ENST00000798091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

ENSG00000303925 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798091.1. 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
	ENSG00000303925	ENST00000798091.1		n.222-402C>A		intron	N/A
	ENSG00000303925	ENST00000798092.1		n.116-402C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 31645 AN: 109546 Hom.: 3977 Cov.: 21

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.289 AC: 31638 AN: 109599 Hom.: 3975 Cov.: 21 AF XY: 0.285 AC XY: 9100 AN XY: 31917

African (AFR) AF: 0.104 AC: 3134 AN: 30060

American (AMR) AF: 0.307 AC: 3156 AN: 10290

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 982 AN: 2620

East Asian (EAS) AF: 0.0826 AC: 289 AN: 3500

South Asian (SAS) AF: 0.315 AC: 807 AN: 2563

European-Finnish (FIN) AF: 0.349 AC: 2006 AN: 5747

Middle Eastern (MID) AF: 0.349 AC: 73 AN: 209

European-Non Finnish (NFE) AF: 0.390 AC: 20489 AN: 52481

Other (OTH) AF: 0.310 AC: 452 AN: 1458

Alfa AF: 0.337 Hom.: 2268

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.86
PhyloP100		0.36

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: rs223686;

hg19: chrX-88758120;