16-65661448-G-T

Variant names:

• chr16-65661448-G-T
• rs1359839

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 0.302 in 152,020 control chromosomes in the GnomAD database, including 7,822 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 0.30 (7822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• 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 (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.302 AC: 45863 AN: 151902 Hom.: 7811 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.302 AC: 45900 AN: 152020 Hom.: 7822 Cov.: 32 AF XY: 0.300 AC XY: 22257 AN XY: 74288

African (AFR) AF: 0.468 AC: 19404 AN: 41444

American (AMR) AF: 0.220 AC: 3356 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3466

East Asian (EAS) AF: 0.0847 AC: 438 AN: 5170

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4812

European-Finnish (FIN) AF: 0.256 AC: 2703 AN: 10568

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16853 AN: 67966

Other (OTH) AF: 0.282 AC: 595 AN: 2112

Alfa AF: 0.266 Hom.: 2951

Bravo AF: 0.301

Asia WGS AF: 0.221 AC: 772 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	0.0010
DANN	Benign	0.50
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1359839; hg19: chr16-65695351;