X-38140399-A-T

Variant names:

• chrX-38140399-A-T
• rs56156506
• ENST00000465127.1:c.172-525722A>T

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.172-525722A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 111,476 control chromosomes in the GnomAD database, including 5,948 homozygotes. There are 10,384 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 0.32 (5948 hom., 10384 hem., cov: 23)
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

ENSG00000250349 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1	c.172-525722A>T		intron_variant	Intron 3 of 8	5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 35855 AN: 111418 Hom.: 5940 Cov.: 23 AF XY: 0.308 AC XY: 10354 AN XY: 33644

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.322 AC: 35890 AN: 111476 Hom.: 5948 Cov.: 23 AF XY: 0.308 AC XY: 10384 AN XY: 33712

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.318

Alfa AF: 0.108 Hom.: 544

Bravo AF: 0.354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs56156506; hg19: chrX-37999652;