chrX-67456553-C-T

Variant names:

• chrX-67456553-C-T
• rs6625187

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 7635 AN: 112140 Hom.: 304 Cov.: 24

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

African (AFR) AF: 0.0119 AC: 370 AN: 31020

American (AMR) AF: 0.0609 AC: 650 AN: 10678

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 205 AN: 2655

East Asian (EAS) AF: 0.291 AC: 1009 AN: 3467

South Asian (SAS) AF: 0.201 AC: 541 AN: 2696

European-Finnish (FIN) AF: 0.0900 AC: 550 AN: 6111

Middle Eastern (MID) AF: 0.0833 AC: 18 AN: 216

European-Non Finnish (NFE) AF: 0.0775 AC: 4120 AN: 53139

Other (OTH) AF: 0.105 AC: 161 AN: 1532

Alfa AF: 0.0788 Hom.: 2359

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs6625187; hg19: chrX-66676395;