rs222800

Variant names:

• chrX-103460338-T-A
• rs222800
• ENST00000445990.2:n.571-877T>A

Your query was ambiguous. Multiple possible variants found:

• chrX-103460338-T-A
• chrX-103460338-T-C
• chrX-103460338-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000445990.2(LL0XNC01-250H12.3):​n.571-877T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 24)
• Consequence: LL0XNC01-250H12.3 ENST00000445990.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

Genes affected

LL0XNC01-250H12.3 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445990.2. 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
	LL0XNC01-250H12.3	NR_188433.1		n.624-877T>A		intron	N/A
	LL0XNC01-250H12.3	NR_188435.1		n.551-877T>A		intron	N/A
	LL0XNC01-250H12.3	NR_188436.1		n.624-877T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LL0XNC01-250H12.3	ENST00000445990.2	TSL:3	n.571-877T>A		intron	N/A
	LL0XNC01-250H12.3	ENST00000628546.2	TSL:5	n.551-877T>A		intron	N/A
	LL0XNC01-250H12.3	ENST00000630831.2	TSL:5	n.610-877T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 24

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

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 6023

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.20
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs222800; hg19: chrX-102715266;