rs6019910

Variant names:

• chr20-49573150-C-T
• rs6019910

Variant summary

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

The variant allele was found at a frequency of 0.157 in 152,166 control chromosomes in the GnomAD database, including 3,285 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 0.16 (3285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23808 AN: 152048 Hom.: 3255 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.157 AC: 23885 AN: 152166 Hom.: 3285 Cov.: 32 AF XY: 0.156 AC XY: 11619 AN XY: 74386

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0848 Hom.: 920

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6019910; hg19: chr20-48189687; COSMIC: COSV59886334;