X-43893123-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 0.0803 in 111,847 control chromosomes in the GnomAD database, including 321 homozygotes. There are 2,609 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 0.080 (321 hom., 2609 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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: 0.0804 AC: 8984 AN: 111795 Hom.: 321 Cov.: 23 AF XY: 0.0769 AC XY: 2610 AN XY: 33949

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0587

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0911

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

GnomAD4 genome AF: 0.0803 AC: 8985 AN: 111847 Hom.: 321 Cov.: 23 AF XY: 0.0767 AC XY: 2609 AN XY: 34011

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0252

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0663 Hom.: 500

Bravo AF: 0.0750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1183035; hg19: chrX-43752369;