X-71186047-T-C

Variant names:

• chrX-71186047-T-C
• rs4844288
• ENST00000450860.1:n.268-2030A>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000450860.1(ENSG00000228427):​n.268-2030A>G 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 0.54 (12572 hom., 12961 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-2030A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.268-2030A>G		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.2	n.322-2034A>G		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.3	n.332-2030A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 54421 AN: 101218 Hom.: 12566 Cov.: 18 AF XY: 0.524 AC XY: 12927 AN XY: 24662

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.580

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: 0.538 AC: 54459 AN: 101254 Hom.: 12572 Cov.: 18 AF XY: 0.525 AC XY: 12961 AN XY: 24708

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.586

Alfa AF: 0.477 Hom.: 3040

Bravo AF: 0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
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: rs4844288; hg19: chrX-70405897;