rs5946324

Variant names:

• chrX-843365-G-C
• rs5946324

Your query was ambiguous. Multiple possible variants found:

• chrX-843365-G-C
• chrX-843365-G-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 0.263 in 151,508 control chromosomes in the GnomAD database, including 5,892 homozygotes. There are 19,511 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 0.26 (5892 hom., 19511 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.264 AC: 39915 AN: 151390 Hom.: 5893 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0211

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.263 AC: 39916 AN: 151508 Hom.: 5892 Cov.: 31 AF XY: 0.264 AC XY: 19511 AN XY: 74008

African (AFR) AF: 0.210 AC: 8648 AN: 41214

American (AMR) AF: 0.197 AC: 3001 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3470

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5164

South Asian (SAS) AF: 0.212 AC: 1017 AN: 4790

European-Finnish (FIN) AF: 0.366 AC: 3854 AN: 10516

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20949 AN: 67844

Other (OTH) AF: 0.249 AC: 521 AN: 2096

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.33
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs5946324; hg19: chrX-804100;