16-48479070-T-C

Position:

• chr16-48479070-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;