chr16-26489697-T-C

Variant names:

• chr16-26489697-T-C
• rs879162

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.465 AC: 19147 AN: 41138

American (AMR) AF: 0.247 AC: 3751 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1102 AN: 5092

South Asian (SAS) AF: 0.182 AC: 873 AN: 4794

European-Finnish (FIN) AF: 0.319 AC: 3327 AN: 10426

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17165 AN: 67854

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.265 Hom.: 18099

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs879162; hg19: chr16-26501018;