rs258595

chr16-55235276-G-A

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 0.667 in 150,702 control chromosomes in the GnomAD database, including 33,752 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 0.67 (33752 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.667 AC: 100499 AN: 150598 Hom.: 33741 Cov.: 28

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.667 AC: 100561 AN: 150702 Hom.: 33752 Cov.: 28 AF XY: 0.670 AC XY: 49286 AN XY: 73542

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.674

Alfa AF: 0.663 Hom.: 4161

Bravo AF: 0.668

Asia WGS AF: 0.785 AC: 2704 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258595; hg19: chr16-55269188;