X-39634466-T-C

Position:

• chrX-39634466-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 111,536 control chromosomes in the GnomAD database, including 6,614 homozygotes. There are 12,545 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 (6614 hom., 12545 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 0.382 AC: 42569 AN: 111482 Hom.: 6623 Cov.: 23 AF XY: 0.372 AC XY: 12540 AN XY: 33688

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.382 AC: 42554 AN: 111536 Hom.: 6614 Cov.: 23 AF XY: 0.372 AC XY: 12545 AN XY: 33752

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.375

Alfa AF: 0.464 Hom.: 12720

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206037; hg19: chrX-39493720;