rs2745851

Positions:

• chr20-17848636-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001754511.2(LOC107985440):​n.226+1529C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778

Genes affected

LOC107985440 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107985440	XR_001754511.2	n.226+1529C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.413

Alfa AF: 0.391 Hom.: 5969

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745851; hg19: chr20-17829280;