X-142842056-G-T

Position:

• chrX-142842056-G-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 0.0982 in 111,902 control chromosomes in the GnomAD database, including 989 homozygotes. There are 3,223 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 0.098 (989 hom., 3223 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 10960 AN: 111850 Hom.: 986 Cov.: 23 AF XY: 0.0940 AC XY: 3200 AN XY: 34052

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0287

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.000490

Gnomad MID AF: 0.0730

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0982 AC: 10994 AN: 111902 Hom.: 989 Cov.: 23 AF XY: 0.0945 AC XY: 3223 AN XY: 34114

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0287

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.000490

Gnomad4 NFE AF: 0.00650

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0184 Hom.: 549

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521831; hg19: chrX-141929842;