X-33765946-A-T

Position:

• chrX-33765946-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668394.1(ENSG00000233928):​n.290+39311A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 111,376 control chromosomes in the GnomAD database, including 1,146 homozygotes. There are 5,008 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 0.15 (1146 hom., 5008 hem., cov: 23)
• Consequence: ENST00000668394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373153	XR_950542.4	n.270+39311A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668394.1	n.290+39311A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 16543 AN: 111321 Hom.: 1148 Cov.: 23 AF XY: 0.149 AC XY: 5010 AN XY: 33521

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.0259

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.148 AC: 16527 AN: 111376 Hom.: 1146 Cov.: 23 AF XY: 0.149 AC XY: 5008 AN XY: 33586

Gnomad4 AFR AF: 0.0289

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.0257

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.146

Alfa AF: 0.178 Hom.: 1067

Bravo AF: 0.136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5928363; hg19: chrX-33784063;