rs2008645

Variant names:

• chr20-48396747-G-A
• rs2008645
• XR_001754655.2:n.1194+392G>A

Variant summary

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

The XR_001754655.2(LOC105372643):​n.1194+392G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,062 control chromosomes in the GnomAD database, including 23,885 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 0.54 (23885 hom., cov: 32)
• Consequence: LOC105372643 XR_001754655.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 2 publications found

Genes affected

LOC105372643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.536 AC: 81423 AN: 151944 Hom.: 23841 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.536 AC: 81536 AN: 152062 Hom.: 23885 Cov.: 32 AF XY: 0.527 AC XY: 39196 AN XY: 74330

African (AFR) AF: 0.779 AC: 32319 AN: 41498

American (AMR) AF: 0.591 AC: 9043 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2723 AN: 5160

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3333 AN: 10568

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28867 AN: 67952

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.479 Hom.: 28224

Bravo AF: 0.575

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.43
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2008645; hg19: chr20-47025490;