rs6019048

Variant names:

• chr20-48331510-T-C
• rs6019048
• ENST00000651871.1:n.789-3381A>G

Variant summary

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

The ENST00000651871.1(ENSG00000286063):​n.789-3381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 152,336 control chromosomes in the GnomAD database, including 196 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 0.036 (196 hom., cov: 32)
• Consequence: ENSG00000286063 ENST00000651871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

ENSG00000286063 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286063	ENST00000651871.1	n.789-3381A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5484 AN: 152218 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0729

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00875

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0362 AC: 5515 AN: 152336 Hom.: 196 Cov.: 32 AF XY: 0.0371 AC XY: 2764 AN XY: 74496

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0246

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.00873

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.0148 Hom.: 52

Bravo AF: 0.0405

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6019048; hg19: chr20-46960253;