X-123182584-T-C

Position:

• chrX-123182584-T-C

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 0.382 in 110,353 control chromosomes in the GnomAD database, including 6,552 homozygotes. There are 12,451 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 0.38 (6552 hom., 12451 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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: 0.381 AC: 42065 AN: 110299 Hom.: 6543 Cov.: 22 AF XY: 0.380 AC XY: 12412 AN XY: 32673

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.382 AC: 42115 AN: 110353 Hom.: 6552 Cov.: 22 AF XY: 0.380 AC XY: 12451 AN XY: 32737

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.409

Alfa AF: 0.306 Hom.: 17038

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	8.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761555; hg19: chrX-122316437;