rs1446224

Variant names:

• chr2-137727463-G-A
• rs1446224

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 0.157 in 135,116 control chromosomes in the GnomAD database, including 2,889 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 0.16 (2889 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.157 AC: 21204 AN: 134988 Hom.: 2872 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.157 AC: 21266 AN: 135116 Hom.: 2889 Cov.: 30 AF XY: 0.160 AC XY: 10634 AN XY: 66572

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0289

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0827 Hom.: 183

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446224; hg19: chr2-138485033;