rs7878993

Variant names:

• chrX-71180543-C-A
• rs7878993

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;