rs4844289

Positions:

• chrX-71188133-A-G
• chrX-71188133-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664514.3(ENSG00000228427):​n.332-4116T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 110,092 control chromosomes in the GnomAD database, including 10,992 homozygotes. There are 16,451 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 0.51 (10992 hom., 16451 hem., cov: 23)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-4116T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664514.3	n.332-4116T>C		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.268-4116T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.322-4120T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.510 AC: 56123 AN: 110037 Hom.: 10985 Cov.: 23 AF XY: 0.507 AC XY: 16400 AN XY: 32333

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.510 AC: 56181 AN: 110092 Hom.: 10992 Cov.: 23 AF XY: 0.508 AC XY: 16451 AN XY: 32398

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.560

Alfa AF: 0.434 Hom.: 4677

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4844289; hg19: chrX-70407983;