rs5964602

chrX-67524554-A-CchrX-67524554-A-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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 37021 AN: 108522 Hom.: 8924 Cov.: 21 AF XY: 0.307 AC XY: 9520 AN XY: 30964

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

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00147

Gnomad4 SAS AF: 0.0830

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.290

Alfa AF: 0.135 Hom.: 809

Bravo AF: 0.366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.89
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5964602; hg19: chrX-66744396;