rs113065570

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 ENST00000653446.1(ENSG00000233928):​n.186-59891C>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 ENST00000653446.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653446.1. 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
	ENSG00000233928	ENST00000439992.6	TSL:5	n.198-59891C>T		intron	N/A
	ENSG00000233928	ENST00000445233.2	TSL:5	n.114+51590C>T		intron	N/A
	ENSG00000233928	ENST00000653446.1		n.186-59891C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs113065570;

hg19: chrX-33811841;