rs5965083

Positions:

• chrX-66010584-G-A
• chrX-66010584-G-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66010584G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.296 AC: 32966 AN: 111486 Hom.: 6394 Cov.: 23 AF XY: 0.277 AC XY: 9361 AN XY: 33734

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

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.000562

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.236

Alfa AF: 0.149 Hom.: 7838

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5965083; hg19: chrX-65230426;