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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450860.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228427	ENST00000450860.1	TSL:3	n.268-3223G>A		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.358-3227G>A		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.600-3223G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6624539;

hg19: chrX-70407090;