X-33793724-C-T

Variant names:

• chrX-33793724-C-T
• rs113065570
• ENST00000439992.6:n.198-59891C>T

Variant summary

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

The ENST00000439992.6(ENSG00000233928):​n.198-59891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 107,622 control chromosomes in the GnomAD database, including 5,467 homozygotes. There are 9,023 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 0.35 (5467 hom., 9023 hem., cov: 23)
• Consequence: ENSG00000233928 ENST00000439992.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 1 publications found

Genes affected

ENSG00000233928 (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 (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373153	XR_950542.4	n.271-59891C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233928	ENST00000439992.6	n.198-59891C>T		intron_variant	Intron 1 of 2	5
ENSG00000233928	ENST00000445233.2	n.114+51590C>T		intron_variant	Intron 1 of 2	5
ENSG00000233928	ENST00000653446.1	n.186-59891C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.350 AC: 37603 AN: 107572 Hom.: 5469 Cov.: 23

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.00227

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.533

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.350 AC: 37624 AN: 107622 Hom.: 5467 Cov.: 23 AF XY: 0.297 AC XY: 9023 AN XY: 30428

African (AFR) AF: 0.395 AC: 11682 AN: 29591

American (AMR) AF: 0.262 AC: 2684 AN: 10259

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1005 AN: 2562

East Asian (EAS) AF: 0.00228 AC: 8 AN: 3509

South Asian (SAS) AF: 0.141 AC: 367 AN: 2607

European-Finnish (FIN) AF: 0.294 AC: 1631 AN: 5551

Middle Eastern (MID) AF: 0.534 AC: 110 AN: 206

European-Non Finnish (NFE) AF: 0.379 AC: 19419 AN: 51219

Other (OTH) AF: 0.362 AC: 529 AN: 1463

Alfa AF: 0.374 Hom.: 2119

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.57
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs113065570; hg19: chrX-33811841;