X-38140399-A-T

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;