chrX-93921725-C-T

Variant names:

• chrX-93921725-C-T
• rs6615574

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 0.405 in 110,137 control chromosomes in the GnomAD database, including 6,511 homozygotes. There are 13,121 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 0.41 (6511 hom., 13121 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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: 0.405 AC: 44601 AN: 110080 Hom.: 6511 Cov.: 23 AF XY: 0.404 AC XY: 13084 AN XY: 32366

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.405 AC: 44638 AN: 110137 Hom.: 6511 Cov.: 23 AF XY: 0.405 AC XY: 13121 AN XY: 32433

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.417

Alfa AF: 0.426 Hom.: 31793

Bravo AF: 0.408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6615574; hg19: chrX-93176724;