rs5959408

Positions:

• chrX-79658774-A-G
• chrX-79658774-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 0.425 in 110,393 control chromosomes in the GnomAD database, including 8,236 homozygotes. There are 13,864 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 0.43 (8236 hom., 13864 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79658774A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.426 AC: 46968 AN: 110342 Hom.: 8242 Cov.: 23 AF XY: 0.425 AC XY: 13858 AN XY: 32634

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.425 AC: 46957 AN: 110393 Hom.: 8236 Cov.: 23 AF XY: 0.424 AC XY: 13864 AN XY: 32695

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.446

Alfa AF: 0.537 Hom.: 53715

Bravo AF: 0.402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5959408; hg19: chrX-78914271;