16-48479070-T-C

Variant names:

• chr16-48479070-T-C
• rs1566467

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 0.536 in 151,840 control chromosomes in the GnomAD database, including 22,555 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 0.54 (22555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.828 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: 0.536 AC: 81376 AN: 151722 Hom.: 22535 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.536 AC: 81436 AN: 151840 Hom.: 22555 Cov.: 31 AF XY: 0.544 AC XY: 40345 AN XY: 74190

African (AFR) AF: 0.625 AC: 25889 AN: 41404

American (AMR) AF: 0.517 AC: 7879 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3462

East Asian (EAS) AF: 0.849 AC: 4383 AN: 5162

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6127 AN: 10532

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31284 AN: 67918

Other (OTH) AF: 0.491 AC: 1032 AN: 2100

Alfa AF: 0.489 Hom.: 24836

Bravo AF: 0.542

Asia WGS AF: 0.647 AC: 2244 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	1.3
DANN	Benign	0.55
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1566467; hg19: chr16-48512981;