rs5964602

Variant names:

• chrX-67524554-A-C
• rs5964602

Your query was ambiguous. Multiple possible variants found:

• chrX-67524554-A-C
• chrX-67524554-A-T

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 0.342 in 108,563 control chromosomes in the GnomAD database, including 8,933 homozygotes. There are 9,563 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 0.34 (8933 hom., 9563 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.341 AC: 37021 AN: 108522 Hom.: 8924 Cov.: 21

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00147

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.342 AC: 37076 AN: 108563 Hom.: 8933 Cov.: 21 AF XY: 0.308 AC XY: 9563 AN XY: 31015

African (AFR) AF: 0.860 AC: 25383 AN: 29500

American (AMR) AF: 0.165 AC: 1679 AN: 10162

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 299 AN: 2613

East Asian (EAS) AF: 0.00147 AC: 5 AN: 3394

South Asian (SAS) AF: 0.0830 AC: 208 AN: 2506

European-Finnish (FIN) AF: 0.112 AC: 634 AN: 5669

Middle Eastern (MID) AF: 0.222 AC: 47 AN: 212

European-Non Finnish (NFE) AF: 0.159 AC: 8310 AN: 52360

Other (OTH) AF: 0.290 AC: 426 AN: 1469

Alfa AF: 0.147 Hom.: 1773

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.49
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs5964602; hg19: chrX-66744396;