XR_928924.3:n.190+757C>T

Variant names:

• chr8-58747717-G-A
• rs2726566
• XR_928924.3:n.190+757C>T

Variant summary

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

The XR_928924.3(LOC105375858):​n.190+757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,096 control chromosomes in the GnomAD database, including 251 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 0.049 (251 hom., cov: 32)
• Consequence: LOC105375858 XR_928924.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

Genes affected

LOC105375858 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 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: 0.0491 AC: 7457 AN: 151978 Hom.: 250 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0876

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0491 AC: 7469 AN: 152096 Hom.: 251 Cov.: 32 AF XY: 0.0494 AC XY: 3676 AN XY: 74368

African (AFR) AF: 0.0202 AC: 838 AN: 41490

American (AMR) AF: 0.0879 AC: 1339 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3470

East Asian (EAS) AF: 0.135 AC: 697 AN: 5174

South Asian (SAS) AF: 0.0407 AC: 196 AN: 4820

European-Finnish (FIN) AF: 0.0205 AC: 217 AN: 10586

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3761 AN: 68000

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0568 Hom.: 449

Bravo AF: 0.0548

Asia WGS AF: 0.101 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2726566; hg19: chr8-59660276;