chrX-146286508-G-A

Variant names:

• chrX-146286508-G-A
• rs6525667

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 0.33 in 110,266 control chromosomes in the GnomAD database, including 4,735 homozygotes. There are 10,703 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 0.33 (4735 hom., 10703 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 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: 0.330 AC: 36362 AN: 110216 Hom.: 4728 Cov.: 23

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.330 AC: 36400 AN: 110266 Hom.: 4735 Cov.: 23 AF XY: 0.328 AC XY: 10703 AN XY: 32594

African (AFR) AF: 0.186 AC: 5669 AN: 30517

American (AMR) AF: 0.493 AC: 5092 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 939 AN: 2620

East Asian (EAS) AF: 0.333 AC: 1132 AN: 3400

South Asian (SAS) AF: 0.336 AC: 863 AN: 2566

European-Finnish (FIN) AF: 0.387 AC: 2249 AN: 5809

Middle Eastern (MID) AF: 0.364 AC: 78 AN: 214

European-Non Finnish (NFE) AF: 0.371 AC: 19529 AN: 52623

Other (OTH) AF: 0.347 AC: 524 AN: 1508

Alfa AF: 0.359 Hom.: 22989

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs6525667; hg19: chrX-145368026;