X-66010584-G-A

Variant names:

• chrX-66010584-G-A
• rs5965083

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 0.296 in 111,537 control chromosomes in the GnomAD database, including 6,398 homozygotes. There are 9,415 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 0.30 (6398 hom., 9415 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 4 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 = 0.714 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: 0.296 AC: 32966 AN: 111486 Hom.: 6394 Cov.: 23

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000560

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.296 AC: 33027 AN: 111537 Hom.: 6398 Cov.: 23 AF XY: 0.279 AC XY: 9415 AN XY: 33795

African (AFR) AF: 0.722 AC: 22038 AN: 30527

American (AMR) AF: 0.206 AC: 2173 AN: 10559

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 285 AN: 2645

East Asian (EAS) AF: 0.000562 AC: 2 AN: 3560

South Asian (SAS) AF: 0.0857 AC: 235 AN: 2742

European-Finnish (FIN) AF: 0.118 AC: 711 AN: 6020

Middle Eastern (MID) AF: 0.162 AC: 35 AN: 216

European-Non Finnish (NFE) AF: 0.131 AC: 6947 AN: 53064

Other (OTH) AF: 0.236 AC: 360 AN: 1528

Alfa AF: 0.185 Hom.: 14976

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.018
DANN	Benign	0.57
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs5965083; hg19: chrX-65230426;