rs1868466

Variant names:

• chr16-77709661-A-C
• rs1868466

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 0.23 in 152,162 control chromosomes in the GnomAD database, including 4,374 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 0.23 (4374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35016 AN: 152044 Hom.: 4365 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.230 AC: 35052 AN: 152162 Hom.: 4374 Cov.: 32 AF XY: 0.228 AC XY: 16951 AN XY: 74392

African (AFR) AF: 0.317 AC: 13168 AN: 41510

American (AMR) AF: 0.207 AC: 3172 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3466

East Asian (EAS) AF: 0.0791 AC: 409 AN: 5172

South Asian (SAS) AF: 0.204 AC: 982 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10590

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14083 AN: 67992

Other (OTH) AF: 0.222 AC: 468 AN: 2112

Alfa AF: 0.227 Hom.: 801

Bravo AF: 0.236

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1868466; hg19: chr16-77743558;