rs6016142

chr20-39672165-C-T

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/exons	MANE	UniProt

Ensembl

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