X-151820659-C-A

Variant names:

• chrX-151820659-C-A
• rs5970126

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 0.155 in 111,179 control chromosomes in the GnomAD database, including 1,399 homozygotes. There are 4,748 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 0.16 (1399 hom., 4748 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 17281 AN: 111128 Hom.: 1397 Cov.: 23

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0279

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0560

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.155 AC: 17284 AN: 111179 Hom.: 1399 Cov.: 23 AF XY: 0.142 AC XY: 4748 AN XY: 33425

African (AFR) AF: 0.311 AC: 9433 AN: 30360

American (AMR) AF: 0.101 AC: 1061 AN: 10548

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 401 AN: 2641

East Asian (EAS) AF: 0.0561 AC: 197 AN: 3509

South Asian (SAS) AF: 0.0826 AC: 214 AN: 2590

European-Finnish (FIN) AF: 0.0522 AC: 316 AN: 6055

Middle Eastern (MID) AF: 0.200 AC: 43 AN: 215

European-Non Finnish (NFE) AF: 0.101 AC: 5341 AN: 53061

Other (OTH) AF: 0.171 AC: 259 AN: 1518

Alfa AF: 0.157 Hom.: 4527

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.79
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs5970126; hg19: chrX-150989131;