XR_925733.4:n.2220-1607C>T

Variant names:

• chr5-5792394-C-T
• rs32566
• XR_925733.4:n.2220-1607C>T

Variant summary

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

The XR_925733.4(LOC105374636):​n.2220-1607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,070 control chromosomes in the GnomAD database, including 6,017 homozygotes. 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 (6017 hom., cov: 32)
• Consequence: LOC105374636 XR_925733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 12 publications found

Genes affected

LOC105374636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.273 AC: 41536 AN: 151950 Hom.: 6002 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.273 AC: 41590 AN: 152070 Hom.: 6017 Cov.: 32 AF XY: 0.273 AC XY: 20318 AN XY: 74336

African (AFR) AF: 0.211 AC: 8738 AN: 41474

American (AMR) AF: 0.382 AC: 5827 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.166 AC: 856 AN: 5170

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3197 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20074 AN: 67974

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.289 Hom.: 29293

Bravo AF: 0.275

Asia WGS AF: 0.230 AC: 802 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs32566; hg19: chr5-5792507;