rs321045

Positions:

• chrX-78412867-C-A
• chrX-78412867-C-G

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 0.37 in 107,746 control chromosomes in the GnomAD database, including 6,851 homozygotes. There are 10,914 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 0.37 (6851 hom., 10914 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.371 AC: 39909 AN: 107697 Hom.: 6858 Cov.: 21 AF XY: 0.362 AC XY: 10909 AN XY: 30169

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.370 AC: 39884 AN: 107746 Hom.: 6851 Cov.: 21 AF XY: 0.361 AC XY: 10914 AN XY: 30232

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.378

Alfa AF: 0.258 Hom.: 1270

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs321045; hg19: chrX-77668364;