rs1998005

Variant names:

• chrX-146309767-A-G
• rs1998005

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 0.418 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 46279 AN: 110667 Hom.: 7119 Cov.: 23

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

African (AFR) AF: 0.303 AC: 9257 AN: 30539

American (AMR) AF: 0.551 AC: 5686 AN: 10314

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1146 AN: 2640

East Asian (EAS) AF: 0.469 AC: 1632 AN: 3481

South Asian (SAS) AF: 0.375 AC: 992 AN: 2646

European-Finnish (FIN) AF: 0.562 AC: 3272 AN: 5826

Middle Eastern (MID) AF: 0.348 AC: 73 AN: 210

European-Non Finnish (NFE) AF: 0.443 AC: 23434 AN: 52875

Other (OTH) AF: 0.438 AC: 661 AN: 1510

Alfa AF: 0.426 Hom.: 13191

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1998005; hg19: chrX-145391285;