rs6638724

Variant names:

• chrX-4388674-G-A
• rs6638724

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;