16-48479070-T-C

Variant names:

• chr16-48479070-T-C
• rs1566467

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.536 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

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.491

Alfa AF: 0.483 Hom.: 18827

Bravo AF: 0.542

Asia WGS AF: 0.647 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1566467; hg19: chr16-48512981;