chrX-74416032-C-T

Variant names:

• chrX-74416032-C-T
• rs527480
• ENST00000797229.1:n.355-471G>A

Variant summary

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

The ENST00000797229.1(ENSG00000303789):​n.355-471G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 110,453 control chromosomes in the GnomAD database, including 6,166 homozygotes. There are 12,224 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 0.37 (6166 hom., 12224 hem., cov: 23)
• Consequence: ENSG00000303789 ENST00000797229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

Genes affected

ENSG00000303789 (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 = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797229.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303789	ENST00000797229.1		n.355-471G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 41145 AN: 110400 Hom.: 6166 Cov.: 23

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.373 AC: 41189 AN: 110453 Hom.: 6166 Cov.: 23 AF XY: 0.374 AC XY: 12224 AN XY: 32719

African (AFR) AF: 0.481 AC: 14586 AN: 30328

American (AMR) AF: 0.272 AC: 2820 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 487 AN: 2630

East Asian (EAS) AF: 0.948 AC: 3297 AN: 3477

South Asian (SAS) AF: 0.430 AC: 1121 AN: 2609

European-Finnish (FIN) AF: 0.422 AC: 2456 AN: 5820

Middle Eastern (MID) AF: 0.220 AC: 46 AN: 209

European-Non Finnish (NFE) AF: 0.298 AC: 15738 AN: 52818

Other (OTH) AF: 0.297 AC: 453 AN: 1524

Alfa AF: 0.327 Hom.: 11827

Bravo AF: 0.370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.28
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs527480; hg19: chrX-73635867;