X-71187240-C-T

Variant names:

• chrX-71187240-C-T
• rs6624539
• ENST00000450860.1:n.268-3223G>A

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.268-3223G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 110,134 control chromosomes in the GnomAD database, including 9,780 homozygotes. There are 15,644 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 0.49 (9780 hom., 15644 hem., cov: 22)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-3223G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.268-3223G>A		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3	n.358-3227G>A		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4	n.600-3223G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 53392 AN: 110081 Hom.: 9772 Cov.: 22

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.485 AC: 53443 AN: 110134 Hom.: 9780 Cov.: 22 AF XY: 0.483 AC XY: 15644 AN XY: 32410

African (AFR) AF: 0.624 AC: 18910 AN: 30301

American (AMR) AF: 0.564 AC: 5766 AN: 10232

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1560 AN: 2632

East Asian (EAS) AF: 0.713 AC: 2462 AN: 3453

South Asian (SAS) AF: 0.546 AC: 1404 AN: 2571

European-Finnish (FIN) AF: 0.363 AC: 2090 AN: 5763

Middle Eastern (MID) AF: 0.605 AC: 130 AN: 215

European-Non Finnish (NFE) AF: 0.378 AC: 19976 AN: 52796

Other (OTH) AF: 0.540 AC: 816 AN: 1510

Alfa AF: 0.433 Hom.: 3794

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs6624539; hg19: chrX-70407090;