rs6019216

Variant names:

• chr20-48468674-G-A
• rs6019216

Your query was ambiguous. Multiple possible variants found:

• chr20-48468674-G-A
• chr20-48468674-G-C

Variant summary

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

The variant allele was found at a frequency of 0.379 in 151,958 control chromosomes in the GnomAD database, including 11,847 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 0.38 (11847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.378 AC: 57453 AN: 151840 Hom.: 11812 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.379 AC: 57540 AN: 151958 Hom.: 11847 Cov.: 32 AF XY: 0.386 AC XY: 28654 AN XY: 74244

African (AFR) AF: 0.510 AC: 21152 AN: 41438

American (AMR) AF: 0.479 AC: 7318 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2560 AN: 5136

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3857 AN: 10564

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19066 AN: 67944

Other (OTH) AF: 0.326 AC: 688 AN: 2110

Alfa AF: 0.308 Hom.: 8343

Bravo AF: 0.395

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6019216; hg19: chr20-47096920;