rs6019910

Variant names:

• chr20-49573150-C-T
• rs6019910

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 0.157 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.157 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

African (AFR) AF: 0.368 AC: 15262 AN: 41486

American (AMR) AF: 0.0834 AC: 1274 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3470

East Asian (EAS) AF: 0.0690 AC: 358 AN: 5186

South Asian (SAS) AF: 0.207 AC: 997 AN: 4824

European-Finnish (FIN) AF: 0.0610 AC: 646 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4439 AN: 68020

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.0955 Hom.: 1624

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.68
PhyloP100		-0.30

Splicing

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

Other links and lift over

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