rs6654819

chrX-6540125-G-A

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 0.17 in 110,634 control chromosomes in the GnomAD database, including 2,507 homozygotes. There are 5,159 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 (2507 hom., 5159 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.170 AC: 18783 AN: 110585 Hom.: 2506 Cov.: 22 AF XY: 0.156 AC XY: 5125 AN XY: 32861

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0621

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0936

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.170 AC: 18821 AN: 110634 Hom.: 2507 Cov.: 22 AF XY: 0.157 AC XY: 5159 AN XY: 32920

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.0960

Gnomad4 ASJ AF: 0.0711

Gnomad4 EAS AF: 0.00114

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.0251

Gnomad4 NFE AF: 0.0583

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0813 Hom.: 4069

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6654819; hg19: chrX-6458166;