X-859810-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 0.0412 in 150,046 control chromosomes in the GnomAD database, including 185 homozygotes. There are 2,991 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 0.041 (185 hom., 2991 hem., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0412 AC: 6184 AN: 149936 Hom.: 186 Cov.: 26 AF XY: 0.0410 AC XY: 2993 AN XY: 73054

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0367

Gnomad EAS AF: 0.000793

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0404

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

GnomAD4 genome AF: 0.0412 AC: 6180 AN: 150046 Hom.: 185 Cov.: 26 AF XY: 0.0409 AC XY: 2991 AN XY: 73176

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.0321

Gnomad4 ASJ AF: 0.0367

Gnomad4 EAS AF: 0.000794

Gnomad4 SAS AF: 0.0459

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0537

Gnomad4 OTH AF: 0.0400

Bravo AF: 0.0390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.7
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35766339; hg19: chrX-820545;