X-67185407-C-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 0.522 in 109,643 control chromosomes in the GnomAD database, including 13,464 homozygotes. There are 16,657 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 0.52 (13464 hom., 16657 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 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: 0.522 AC: 57239 AN: 109589 Hom.: 13472 Cov.: 23 AF XY: 0.520 AC XY: 16645 AN XY: 32023

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.522 AC: 57230 AN: 109643 Hom.: 13464 Cov.: 23 AF XY: 0.519 AC XY: 16657 AN XY: 32087

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.520

Alfa AF: 0.653 Hom.: 27939

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.1
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34191540; hg19: chrX-66405249;