16-48882643-C-G

Position:

• chr16-48882643-C-G

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 0.283 in 151,944 control chromosomes in the GnomAD database, including 6,567 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 0.28 (6567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42926 AN: 151826 Hom.: 6556 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.283 AC: 42980 AN: 151944 Hom.: 6567 Cov.: 32 AF XY: 0.286 AC XY: 21213 AN XY: 74260

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.267

Alfa AF: 0.137 Hom.: 234

Bravo AF: 0.281

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11860830; hg19: chr16-48916554;