X-93921725-C-T

Variant names:

• chrX-93921725-C-T
• rs6615574

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 0.405 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.355 AC: 10747 AN: 30313

American (AMR) AF: 0.412 AC: 4252 AN: 10320

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 840 AN: 2625

East Asian (EAS) AF: 0.428 AC: 1483 AN: 3464

South Asian (SAS) AF: 0.418 AC: 1099 AN: 2628

European-Finnish (FIN) AF: 0.457 AC: 2589 AN: 5664

Middle Eastern (MID) AF: 0.610 AC: 130 AN: 213

European-Non Finnish (NFE) AF: 0.427 AC: 22537 AN: 52754

Other (OTH) AF: 0.417 AC: 621 AN: 1488

Alfa AF: 0.421 Hom.: 39965

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6615574; hg19: chrX-93176724;