rs6016142

Variant names:

• chr20-39672165-C-T
• rs6016142

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.0791 in 152,262 control chromosomes in the GnomAD database, including 595 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 0.079 (595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12048 AN: 152144 Hom.: 598 Cov.: 33

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0764

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0791 AC: 12045 AN: 152262 Hom.: 595 Cov.: 33 AF XY: 0.0778 AC XY: 5795 AN XY: 74444

African (AFR) AF: 0.0331 AC: 1374 AN: 41550

American (AMR) AF: 0.0735 AC: 1124 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3472

East Asian (EAS) AF: 0.0764 AC: 395 AN: 5168

South Asian (SAS) AF: 0.133 AC: 643 AN: 4824

European-Finnish (FIN) AF: 0.0577 AC: 612 AN: 10606

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7126 AN: 68032

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0986 Hom.: 2534

Bravo AF: 0.0770

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	20
DANN	Benign	0.77
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6016142; hg19: chr20-38300807;