rs6625187

chrX-67456553-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 0.0681 in 112,195 control chromosomes in the GnomAD database, including 309 homozygotes. There are 2,455 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 0.068 (309 hom., 2455 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.0681 AC: 7635 AN: 112140 Hom.: 304 Cov.: 24 AF XY: 0.0714 AC XY: 2451 AN XY: 34306

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0279

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0844

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0681 AC: 7643 AN: 112195 Hom.: 309 Cov.: 24 AF XY: 0.0714 AC XY: 2455 AN XY: 34371

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0609

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0900

Gnomad4 NFE AF: 0.0775

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0792 Hom.: 1707

Bravo AF: 0.0671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6625187; hg19: chrX-66676395;