rs1884641

Variant names:

• chr20-6059263-A-C
• rs1884641
• XR_007067512.1:n.*230T>G

Variant summary

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

The XR_007067512.1(LOC124904865):​n.*230T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,252 control chromosomes in the GnomAD database, including 4,133 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 0.21 (4133 hom., cov: 33)
• Consequence: LOC124904865 XR_007067512.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

Genes affected

LOC124904865 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904865	XR_007067512.1	n.*230T>G		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31241 AN: 152134 Hom.: 4127 Cov.: 33

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.205 AC: 31261 AN: 152252 Hom.: 4133 Cov.: 33 AF XY: 0.205 AC XY: 15274 AN XY: 74438

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.221

Alfa AF: 0.245 Hom.: 9960

Bravo AF: 0.214

Asia WGS AF: 0.360 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884641; hg19: chr20-6039909;