chrX-4388674-G-A

Position:

• chrX-4388674-G-A

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 0.169 in 108,729 control chromosomes in the GnomAD database, including 3,178 homozygotes. There are 4,785 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 0.17 (3178 hom., 4785 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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 = 0.5 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: 0.168 AC: 18287 AN: 108686 Hom.: 3173 Cov.: 21 AF XY: 0.152 AC XY: 4752 AN XY: 31170

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.00991

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0515

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.169 AC: 18339 AN: 108729 Hom.: 3178 Cov.: 21 AF XY: 0.153 AC XY: 4785 AN XY: 31225

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.00991

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.00505

Gnomad4 OTH AF: 0.145

Alfa AF: 0.108 Hom.: 754

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6638724; hg19: chrX-4306715; COSMIC: COSV54750748;