X-1897825-C-G

Variant names:

• chrX-1897825-C-G
• rs6644913

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 0.51 in 151,886 control chromosomes in the GnomAD database, including 20,060 homozygotes. There are 37,762 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 0.51 (20060 hom., 37762 hem., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.510 AC: 77392 AN: 151766 Hom.: 20037 Cov.: 33 AF XY: 0.509 AC XY: 37685 AN XY: 74074

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.510 AC: 77474 AN: 151886 Hom.: 20060 Cov.: 33 AF XY: 0.509 AC XY: 37762 AN XY: 74204

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.471

Bravo AF: 0.505

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6644913; hg19: chrX-2016718;