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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985440	XR_001754511.2	n.226+1529C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;