XR_943790.3:n.829+10096T>G

Variant names:

• chr14-40602267-A-C
• rs2050483
• XR_943790.3:n.829+10096T>G

Variant summary

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

The XR_943790.3(LOC105370466):​n.829+10096T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,000 control chromosomes in the GnomAD database, including 18,357 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 0.48 (18357 hom., cov: 33)
• Consequence: LOC105370466 XR_943790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 2 publications found

Genes affected

LOC105370466 (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 (AFR) allele frequency at 95% confidence interval = 0.655 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: 0.476 AC: 72335 AN: 151880 Hom.: 18335 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.476 AC: 72413 AN: 152000 Hom.: 18357 Cov.: 33 AF XY: 0.480 AC XY: 35653 AN XY: 74292

African (AFR) AF: 0.661 AC: 27432 AN: 41470

American (AMR) AF: 0.460 AC: 7019 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2781 AN: 5166

South Asian (SAS) AF: 0.512 AC: 2472 AN: 4826

European-Finnish (FIN) AF: 0.390 AC: 4120 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25513 AN: 67944

Other (OTH) AF: 0.454 AC: 957 AN: 2106

Alfa AF: 0.433 Hom.: 1993

Bravo AF: 0.490

Asia WGS AF: 0.533 AC: 1854 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	1.4
DANN	Benign	0.90
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2050483; hg19: chr14-41071472;