chr16-48882643-C-G

Variant names:

• chr16-48882643-C-G
• rs11860830

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 0.283 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.383 AC: 15838 AN: 41398

American (AMR) AF: 0.291 AC: 4457 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1030 AN: 5148

South Asian (SAS) AF: 0.394 AC: 1894 AN: 4810

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10574

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15208 AN: 67934

Other (OTH) AF: 0.267 AC: 564 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs11860830; hg19: chr16-48916554;