rs879162

chr16-26489697-T-C

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 0.31 in 151,264 control chromosomes in the GnomAD database, including 8,052 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 0.31 (8052 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.310 AC: 46845 AN: 151146 Hom.: 8030 Cov.: 29

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.310 AC: 46912 AN: 151264 Hom.: 8052 Cov.: 29 AF XY: 0.308 AC XY: 22749 AN XY: 73860

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.289

Alfa AF: 0.250 Hom.: 10094

Bravo AF: 0.316

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.0
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879162; hg19: chr16-26501018;