rs4825220

Positions:

• chrX-140132319-A-G
• chrX-140132319-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 0.388 in 110,451 control chromosomes in the GnomAD database, including 7,238 homozygotes. There are 12,638 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 0.39 (7238 hom., 12638 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.388 AC: 42858 AN: 110408 Hom.: 7237 Cov.: 22 AF XY: 0.387 AC XY: 12639 AN XY: 32650

Gnomad AFR AF: 0.0994

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.388 AC: 42851 AN: 110451 Hom.: 7238 Cov.: 22 AF XY: 0.386 AC XY: 12638 AN XY: 32703

Gnomad4 AFR AF: 0.0991

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.404

Alfa AF: 0.473 Hom.: 10114

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4825220; hg19: chrX-139214478;