XR_946435.2:n.188+2320A>G

Variant names:

• chr10-125265767-A-G
• rs875748
• XR_946435.2:n.188+2320A>G

Variant summary

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

The XR_946435.2(LOC105378542):​n.188+2320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,112 control chromosomes in the GnomAD database, including 10,621 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 0.33 (10621 hom., cov: 33)
• Consequence: LOC105378542 XR_946435.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 0 publications found

Genes affected

LOC105378542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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: 0.332 AC: 50498 AN: 151994 Hom.: 10584 Cov.: 33

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.333 AC: 50591 AN: 152112 Hom.: 10621 Cov.: 33 AF XY: 0.329 AC XY: 24460 AN XY: 74386

African (AFR) AF: 0.601 AC: 24909 AN: 41452

American (AMR) AF: 0.231 AC: 3537 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 998 AN: 3472

East Asian (EAS) AF: 0.0485 AC: 251 AN: 5172

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2715 AN: 10594

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16260 AN: 67988

Other (OTH) AF: 0.297 AC: 629 AN: 2116

Alfa AF: 0.291 Hom.: 1017

Bravo AF: 0.342

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.81
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs875748; hg19: chr10-126954336;