chr16-19922278-C-T

Variant names:

• chr16-19922278-C-T
• rs12444979

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 0.111 in 152,056 control chromosomes in the GnomAD database, including 1,038 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 0.11 (1038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.111 AC: 16832 AN: 151938 Hom.: 1039 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.111 AC: 16840 AN: 152056 Hom.: 1038 Cov.: 32 AF XY: 0.108 AC XY: 7999 AN XY: 74308

Gnomad4 AFR AF: 0.0869

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0442

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.107

Alfa AF: 0.130 Hom.: 2377

Bravo AF: 0.108

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12444979; hg19: chr16-19933600;