rs276960

chr16-86203798-C-T

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 0.875 in 152,142 control chromosomes in the GnomAD database, including 58,337 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 0.87 (58337 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.875 AC: 133037 AN: 152024 Hom.: 58303 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.875 AC: 133124 AN: 152142 Hom.: 58337 Cov.: 31 AF XY: 0.874 AC XY: 65011 AN XY: 74380

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.883

Alfa AF: 0.875 Hom.: 7243

Bravo AF: 0.877

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs276960; hg19: chr16-86237404;