rs28386840

chr16-55652906-T-Achr16-55652906-T-Cchr16-55652906-T-G

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 0.639 in 145,034 control chromosomes in the GnomAD database, including 29,748 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 0.64 (29748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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: 0.639 AC: 92600 AN: 144926 Hom.: 29725 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.639 AC: 92666 AN: 145034 Hom.: 29748 Cov.: 32 AF XY: 0.644 AC XY: 45735 AN XY: 70978

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.644

Alfa AF: 0.367 Hom.: 530

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28386840; hg19: chr16-55686818;