rs5979778

chrX-12965184-A-GchrX-12965184-A-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 0.325 in 110,621 control chromosomes in the GnomAD database, including 4,686 homozygotes. There are 10,294 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 0.32 (4686 hom., 10294 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.325 AC: 35929 AN: 110565 Hom.: 4685 Cov.: 22 AF XY: 0.313 AC XY: 10283 AN XY: 32827

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.325 AC: 35943 AN: 110621 Hom.: 4686 Cov.: 22 AF XY: 0.313 AC XY: 10294 AN XY: 32893

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.322

Alfa AF: 0.395 Hom.: 24056

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	3.7
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5979778; hg19: chrX-12983303;