X-43071165-G-A

Variant names:

• chrX-43071165-G-A
• rs5991441

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 0.0592 in 111,579 control chromosomes in the GnomAD database, including 353 homozygotes. There are 1,844 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 0.059 (353 hom., 1844 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 6594 AN: 111532 Hom.: 351 Cov.: 22

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.00719

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0126

Gnomad NFE AF: 0.00653

Gnomad OTH AF: 0.0553

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

GnomAD4 genome AF: 0.0592 AC: 6608 AN: 111579 Hom.: 353 Cov.: 22 AF XY: 0.0546 AC XY: 1844 AN XY: 33801

African (AFR) AF: 0.149 AC: 4558 AN: 30636

American (AMR) AF: 0.0420 AC: 442 AN: 10525

Ashkenazi Jewish (ASJ) AF: 0.00719 AC: 19 AN: 2643

East Asian (EAS) AF: 0.241 AC: 843 AN: 3495

South Asian (SAS) AF: 0.0515 AC: 137 AN: 2659

European-Finnish (FIN) AF: 0.0293 AC: 177 AN: 6048

Middle Eastern (MID) AF: 0.0138 AC: 3 AN: 218

European-Non Finnish (NFE) AF: 0.00653 AC: 347 AN: 53146

Other (OTH) AF: 0.0539 AC: 82 AN: 1521

Alfa AF: 0.0228 Hom.: 379

Bravo AF: 0.0725

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.49
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs5991441; hg19: chrX-42930414;