rs6644384

chrX-861504-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 0.42 in 149,068 control chromosomes in the GnomAD database, including 17,250 homozygotes. There are 31,174 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 0.42 (17250 hom., 31174 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -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 = 0.923 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: 0.420 AC: 62560 AN: 148950 Hom.: 17235 Cov.: 30 AF XY: 0.430 AC XY: 31129 AN XY: 72472

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.420 AC: 62597 AN: 149068 Hom.: 17250 Cov.: 30 AF XY: 0.429 AC XY: 31174 AN XY: 72600

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.74
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6644384; hg19: chrX-822239;