rs2745851

Variant names:

• chr20-17848636-G-A
• rs2745851
• XR_001754511.2:n.226+1529C>T

Variant summary

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

The XR_001754511.2(LOC107985440):​n.226+1529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,100 control chromosomes in the GnomAD database, including 18,866 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 0.47 (18866 hom., cov: 33)
• Consequence: LOC107985440 XR_001754511.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 8 publications found

Genes affected

LOC107985440 (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 (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.471 AC: 71621 AN: 151982 Hom.: 18827 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.471 AC: 71713 AN: 152100 Hom.: 18866 Cov.: 33 AF XY: 0.468 AC XY: 34799 AN XY: 74374

African (AFR) AF: 0.721 AC: 29896 AN: 41476

American (AMR) AF: 0.406 AC: 6208 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 952 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2791 AN: 5172

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4820

European-Finnish (FIN) AF: 0.390 AC: 4132 AN: 10584

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.365 AC: 24781 AN: 67968

Other (OTH) AF: 0.413 AC: 873 AN: 2114

Alfa AF: 0.411 Hom.: 25701

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.22
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs2745851; hg19: chr20-17829280;