rs5965083

Variant names:

• chrX-66010584-G-A
• rs5965083

Your query was ambiguous. Multiple possible variants found:

• 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;