chrX-147961254-C-T

Position:

• chrX-147961254-C-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 0.133 in 111,310 control chromosomes in the GnomAD database, including 1,314 homozygotes. There are 4,091 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 (1314 hom., 4091 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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 = 0.319 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: 0.133 AC: 14820 AN: 111258 Hom.: 1316 Cov.: 23 AF XY: 0.122 AC XY: 4080 AN XY: 33496

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.00198

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.133 AC: 14826 AN: 111310 Hom.: 1314 Cov.: 23 AF XY: 0.122 AC XY: 4091 AN XY: 33558

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0423

Gnomad4 EAS AF: 0.00198

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0664

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0805 Hom.: 2363

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5904818; hg19: chrX-147042774;