X-71190650-C-T

Variant names:

• chrX-71190650-C-T
• rs4844146
• ENST00000450860.1:n.268-6633G>A

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.268-6633G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 110,563 control chromosomes in the GnomAD database, including 10,561 homozygotes. There are 16,335 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 0.50 (10561 hom., 16335 hem., cov: 23)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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.268-6633G>A		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.358-6637G>A		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.600-6633G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 55390 AN: 110508 Hom.: 10553 Cov.: 23

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.501 AC: 55445 AN: 110563 Hom.: 10561 Cov.: 23 AF XY: 0.498 AC XY: 16335 AN XY: 32821

African (AFR) AF: 0.666 AC: 20214 AN: 30373

American (AMR) AF: 0.575 AC: 5933 AN: 10310

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 1579 AN: 2626

East Asian (EAS) AF: 0.713 AC: 2486 AN: 3489

South Asian (SAS) AF: 0.560 AC: 1483 AN: 2650

European-Finnish (FIN) AF: 0.360 AC: 2122 AN: 5895

Middle Eastern (MID) AF: 0.596 AC: 127 AN: 213

European-Non Finnish (NFE) AF: 0.385 AC: 20325 AN: 52838

Other (OTH) AF: 0.555 AC: 836 AN: 1506

Alfa AF: 0.438 Hom.: 55729

Bravo AF: 0.528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.81
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4844146; hg19: chrX-70410500;