rs7878993

chrX-71180543-C-A

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 0.399 in 111,432 control chromosomes in the GnomAD database, including 7,474 homozygotes. There are 12,819 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 0.40 (7474 hom., 12819 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 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: 0.399 AC: 44466 AN: 111379 Hom.: 7474 Cov.: 23 AF XY: 0.380 AC XY: 12783 AN XY: 33607

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.399 AC: 44501 AN: 111432 Hom.: 7474 Cov.: 23 AF XY: 0.381 AC XY: 12819 AN XY: 33670

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.423

Alfa AF: 0.368 Hom.: 4045

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.53
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7878993; hg19: chrX-70400393;