rs6016142

Variant names:

• chr20-39672165-C-T
• rs6016142

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0792 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

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.0735

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0764

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0577

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.104 Hom.: 997

Bravo AF: 0.0770

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6016142; hg19: chr20-38300807;