X-67506664-A-G

Position:

• chrX-67506664-A-G

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 0.343 in 110,194 control chromosomes in the GnomAD database, including 8,955 homozygotes. There are 10,257 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 0.34 (8955 hom., 10257 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.343 AC: 37771 AN: 110143 Hom.: 8946 Cov.: 23 AF XY: 0.314 AC XY: 10207 AN XY: 32455

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.00170

Gnomad SAS AF: 0.0811

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.343 AC: 37833 AN: 110194 Hom.: 8955 Cov.: 23 AF XY: 0.315 AC XY: 10257 AN XY: 32516

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.00170

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.291

Alfa AF: 0.0792 Hom.: 364

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.39
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525177; hg19: chrX-66726506;