X-123858846-G-C

Variant names:

• chrX-123858846-G-C
• rs5956578

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.39 (6437 hom., 6565 hem., cov: 16)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.387 AC: 36652 AN: 94785 Hom.: 6433 Cov.: 16

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.387 AC: 36660 AN: 94796 Hom.: 6437 Cov.: 16 AF XY: 0.316 AC XY: 6565 AN XY: 20806

African (AFR) AF: 0.516 AC: 12818 AN: 24835

American (AMR) AF: 0.351 AC: 2879 AN: 8204

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 869 AN: 2459

East Asian (EAS) AF: 0.0742 AC: 233 AN: 3140

South Asian (SAS) AF: 0.165 AC: 330 AN: 1996

European-Finnish (FIN) AF: 0.329 AC: 1173 AN: 3569

Middle Eastern (MID) AF: 0.354 AC: 64 AN: 181

European-Non Finnish (NFE) AF: 0.364 AC: 17690 AN: 48576

Other (OTH) AF: 0.370 AC: 451 AN: 1220

Alfa AF: 0.383 Hom.: 2143

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.25
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5956578;

hg19: chrX-122992696;