chrX-51424836-T-A

Position:

• chrX-51424836-T-A

Variant summary

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

The ENST00000455931.2(ENSG00000226530):​n.757+28155T>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 0.328 in 109,529 control chromosomes in the GnomAD database, including 4,720 homozygotes. There are 9,962 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 0.33 (4720 hom., 9962 hem., cov: 22)
• Consequence: ENST00000455931.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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.757+28155T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 35899 AN: 109482 Hom.: 4714 Cov.: 22 AF XY: 0.311 AC XY: 9921 AN XY: 31918

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.328 AC: 35944 AN: 109529 Hom.: 4720 Cov.: 22 AF XY: 0.312 AC XY: 9962 AN XY: 31975

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0595

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.306

Alfa AF: 0.332 Hom.: 2149

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972635; hg19: chrX-51167688;