16-20246545-C-T

Variant names:

• chr16-20246545-C-T
• rs12597579

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 0.073 in 152,156 control chromosomes in the GnomAD database, including 530 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 0.073 (530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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: 0.0729 AC: 11083 AN: 152038 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0730 AC: 11104 AN: 152156 Hom.: 530 Cov.: 32 AF XY: 0.0762 AC XY: 5667 AN XY: 74382

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0609

Alfa AF: 0.0553 Hom.: 308

Bravo AF: 0.0757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12597579; hg19: chr16-20257867;