rs5934507

Variant names:

• chrX-8949165-A-G
• rs5934507

Your query was ambiguous. Multiple possible variants found:

• chrX-8949165-A-G
• chrX-8949165-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 0.271 in 109,257 control chromosomes in the GnomAD database, including 3,089 homozygotes. There are 8,128 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 0.27 (3089 hom., 8128 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 29552 AN: 109207 Hom.: 3089 Cov.: 21

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.271 AC: 29563 AN: 109257 Hom.: 3089 Cov.: 21 AF XY: 0.257 AC XY: 8128 AN XY: 31623

African (AFR) AF: 0.321 AC: 9613 AN: 29986

American (AMR) AF: 0.179 AC: 1840 AN: 10263

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1132 AN: 2611

East Asian (EAS) AF: 0.237 AC: 799 AN: 3367

South Asian (SAS) AF: 0.219 AC: 554 AN: 2532

European-Finnish (FIN) AF: 0.192 AC: 1081 AN: 5638

Middle Eastern (MID) AF: 0.351 AC: 72 AN: 205

European-Non Finnish (NFE) AF: 0.266 AC: 13973 AN: 52490

Other (OTH) AF: 0.279 AC: 416 AN: 1491

Alfa AF: 0.274 Hom.: 1687

Bravo AF: 0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.8
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs5934507; hg19: chrX-8917206;