rs5931921

Variant names:

• chrX-127293968-C-T
• rs5931921
• XR_001755952.1:n.187+89G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001755952.1(LOC107985709):​n.187+89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 109,352 control chromosomes in the GnomAD database, including 2,053 homozygotes. There are 6,794 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 0.22 (2053 hom., 6794 hem., cov: 21)
• Consequence: LOC107985709 XR_001755952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 0 publications found

Genes affected

LOC107985709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 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: 0.216 AC: 23583 AN: 109303 Hom.: 2052 Cov.: 21

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0236

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.216 AC: 23588 AN: 109352 Hom.: 2053 Cov.: 21 AF XY: 0.213 AC XY: 6794 AN XY: 31938

African (AFR) AF: 0.147 AC: 4435 AN: 30221

American (AMR) AF: 0.325 AC: 3299 AN: 10156

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 420 AN: 2607

East Asian (EAS) AF: 0.0234 AC: 81 AN: 3457

South Asian (SAS) AF: 0.145 AC: 376 AN: 2592

European-Finnish (FIN) AF: 0.338 AC: 1903 AN: 5638

Middle Eastern (MID) AF: 0.181 AC: 39 AN: 215

European-Non Finnish (NFE) AF: 0.238 AC: 12456 AN: 52312

Other (OTH) AF: 0.211 AC: 314 AN: 1487

Alfa AF: 0.234 Hom.: 7175

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.43
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs5931921; hg19: chrX-126427951;