chrX-51458235-C-A

Position:

• chrX-51458235-C-A

Variant summary

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

The ENST00000455931.2(ENSG00000226530):​n.758-7172C>A 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 0.134 in 111,841 control chromosomes in the GnomAD database, including 948 homozygotes. There are 4,519 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 0.13 (948 hom., 4519 hem., cov: 23)
• Consequence: ENST00000455931.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000455931.2	n.758-7172C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 15006 AN: 111790 Hom.: 948 Cov.: 23 AF XY: 0.133 AC XY: 4511 AN XY: 34014

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.134 AC: 15012 AN: 111841 Hom.: 948 Cov.: 23 AF XY: 0.133 AC XY: 4519 AN XY: 34077

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.125

Alfa AF: 0.156 Hom.: 2896

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945608; hg19: chrX-51201087;