rs1998005

Positions:

• chrX-146309767-A-G

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 0.418 in 110,720 control chromosomes in the GnomAD database, including 7,123 homozygotes. There are 13,872 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 (7123 hom., 13872 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 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: 0.418 AC: 46279 AN: 110667 Hom.: 7119 Cov.: 23 AF XY: 0.420 AC XY: 13836 AN XY: 32925

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.418 AC: 46320 AN: 110720 Hom.: 7123 Cov.: 23 AF XY: 0.421 AC XY: 13872 AN XY: 32988

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.438

Alfa AF: 0.429 Hom.: 8307

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998005; hg19: chrX-145391285;