16-28064578-C-T

Variant names:

• chr16-28064578-C-T
• rs205420

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 0.74 in 151,970 control chromosomes in the GnomAD database, including 41,718 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 0.74 (41718 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.740 AC: 112371 AN: 151852 Hom.: 41680 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.740 AC: 112467 AN: 151970 Hom.: 41718 Cov.: 31 AF XY: 0.743 AC XY: 55164 AN XY: 74256

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.731

Alfa AF: 0.726 Hom.: 5286

Bravo AF: 0.743

Asia WGS AF: 0.850 AC: 2955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs205420; hg19: chr16-28075899;