rs6019910

chr20-49573150-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;