16-26877032-A-G

Variant names:

• chr16-26877032-A-G
• rs2521669

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 0.898 in 152,164 control chromosomes in the GnomAD database, including 62,169 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 0.90 (62169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136579 AN: 152046 Hom.: 62130 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.971

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.898 AC: 136669 AN: 152164 Hom.: 62169 Cov.: 32 AF XY: 0.897 AC XY: 66731 AN XY: 74366

African (AFR) AF: 0.769 AC: 31867 AN: 41462

American (AMR) AF: 0.920 AC: 14065 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3375 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3530 AN: 5158

South Asian (SAS) AF: 0.878 AC: 4227 AN: 4812

European-Finnish (FIN) AF: 0.987 AC: 10483 AN: 10618

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.971 AC: 66037 AN: 68028

Other (OTH) AF: 0.897 AC: 1899 AN: 2116

Alfa AF: 0.942 Hom.: 212796

Bravo AF: 0.888

Asia WGS AF: 0.789 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.83
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2521669; hg19: chr16-26888353;