rs6654819

Variant names:

• chrX-6540125-G-A
• rs6654819

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;