chrX-106250703-G-A

Variant names:

• chrX-106250703-G-A
• rs379742

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 0.175 in 110,723 control chromosomes in the GnomAD database, including 1,582 homozygotes. There are 5,762 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 0.17 (1582 hom., 5762 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.175 AC: 19359 AN: 110671 Hom.: 1583 Cov.: 22

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.175 AC: 19362 AN: 110723 Hom.: 1582 Cov.: 22 AF XY: 0.174 AC XY: 5762 AN XY: 33101

African (AFR) AF: 0.0538 AC: 1647 AN: 30608

American (AMR) AF: 0.288 AC: 3002 AN: 10419

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 325 AN: 2633

East Asian (EAS) AF: 0.393 AC: 1352 AN: 3440

South Asian (SAS) AF: 0.331 AC: 862 AN: 2604

European-Finnish (FIN) AF: 0.192 AC: 1135 AN: 5925

Middle Eastern (MID) AF: 0.155 AC: 33 AN: 213

European-Non Finnish (NFE) AF: 0.200 AC: 10529 AN: 52694

Other (OTH) AF: 0.184 AC: 278 AN: 1513

Alfa AF: 0.190 Hom.: 14073

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		0.36

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: rs379742;

hg19: chrX-105493919;