chrX-1897825-C-G

Variant names:

• chrX-1897825-C-G
• rs6644913

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 0.51 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77392 AN: 151766 Hom.: 20037 Cov.: 33

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

African (AFR) AF: 0.594 AC: 24632 AN: 41486

American (AMR) AF: 0.437 AC: 6667 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1297 AN: 3462

East Asian (EAS) AF: 0.521 AC: 2660 AN: 5102

South Asian (SAS) AF: 0.355 AC: 1701 AN: 4798

European-Finnish (FIN) AF: 0.607 AC: 6415 AN: 10576

Middle Eastern (MID) AF: 0.319 AC: 92 AN: 288

European-Non Finnish (NFE) AF: 0.481 AC: 32643 AN: 67896

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Bravo AF: 0.505

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.61
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6644913; hg19: chrX-2016718;