X-103460338-T-C

Variant names:

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

Variant summary

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

The ENST00000445990.2(LL0XNC01-250H12.3):​n.571-877T>C 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 0.80 (24969 hom., 27416 hem., cov: 24)
  • Failed GnomAD Quality Control
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

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>C		intron	N/A
	LL0XNC01-250H12.3	NR_188435.1		n.551-877T>C		intron	N/A
	LL0XNC01-250H12.3	NR_188436.1		n.624-877T>C		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>C		intron	N/A
	LL0XNC01-250H12.3	ENST00000628546.2	TSL:5	n.551-877T>C		intron	N/A
	LL0XNC01-250H12.3	ENST00000630831.2	TSL:5	n.610-877T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 89395 AN: 111074 Hom.: 24969 Cov.: 24

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.792

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: 0.805 AC: 89447 AN: 111126 Hom.: 24969 Cov.: 24 AF XY: 0.823 AC XY: 27416 AN XY: 33322

African (AFR) AF: 0.895 AC: 27463 AN: 30691

American (AMR) AF: 0.854 AC: 9042 AN: 10590

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 1961 AN: 2628

East Asian (EAS) AF: 0.994 AC: 3504 AN: 3525

South Asian (SAS) AF: 0.880 AC: 2319 AN: 2635

European-Finnish (FIN) AF: 0.832 AC: 4952 AN: 5952

Middle Eastern (MID) AF: 0.752 AC: 158 AN: 210

European-Non Finnish (NFE) AF: 0.727 AC: 38308 AN: 52711

Other (OTH) AF: 0.795 AC: 1203 AN: 1514

Alfa AF: 0.764 Hom.: 6023

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.18
PhyloP100		-1.4

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: rs222800;

hg19: chrX-102715266;