rs5959408

Variant names:

• chrX-79658774-A-G
• rs5959408

Your query was ambiguous. Multiple possible variants found:

• chrX-79658774-A-G
• chrX-79658774-A-T

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.426 AC: 46968 AN: 110342 Hom.: 8242 Cov.: 23

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

African (AFR) AF: 0.169 AC: 5151 AN: 30523

American (AMR) AF: 0.370 AC: 3854 AN: 10408

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1265 AN: 2630

East Asian (EAS) AF: 0.487 AC: 1678 AN: 3449

South Asian (SAS) AF: 0.602 AC: 1554 AN: 2583

European-Finnish (FIN) AF: 0.496 AC: 2822 AN: 5690

Middle Eastern (MID) AF: 0.505 AC: 108 AN: 214

European-Non Finnish (NFE) AF: 0.562 AC: 29653 AN: 52722

Other (OTH) AF: 0.446 AC: 670 AN: 1503

Alfa AF: 0.511 Hom.: 64636

Bravo AF: 0.402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs5959408; hg19: chrX-78914271;