rs6019048

Positions:

• chr20-48331510-T-C

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, non coding transcript 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: ENST00000651871.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651871.1	n.789-3381A>G		intron_variant, non_coding_transcript_variant

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;