rs12444268

Variant names:

• chr16-20331250-T-A
• rs12444268

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 0.219 in 152,140 control chromosomes in the GnomAD database, including 4,291 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 0.22 (4291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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: 0.220 AC: 33382 AN: 152022 Hom.: 4291 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.219 AC: 33377 AN: 152140 Hom.: 4291 Cov.: 32 AF XY: 0.216 AC XY: 16098 AN XY: 74366

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.205

Alfa AF: 0.276 Hom.: 3376

Bravo AF: 0.206

Asia WGS AF: 0.0810 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12444268; hg19: chr16-20342572;