rs12449237

Variant names:

• chr16-62225701-G-T
• rs12449237

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 0.277 in 151,988 control chromosomes in the GnomAD database, including 6,442 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 (6442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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 (EAS) allele frequency at 95% confidence interval = 0.627 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: 0.277 AC: 42091 AN: 151870 Hom.: 6429 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.277 AC: 42141 AN: 151988 Hom.: 6442 Cov.: 32 AF XY: 0.286 AC XY: 21258 AN XY: 74300

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.274

Alfa AF: 0.242 Hom.: 9896

Bravo AF: 0.284

Asia WGS AF: 0.506 AC: 1758 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	0.57
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12449237; hg19: chr16-62259605;