rs5979778

Variant names:

• chrX-12965184-A-G
• rs5979778

Your query was ambiguous. Multiple possible variants found:

• chrX-12965184-A-G
• chrX-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;