rs3212247

Variant names:

• chr14-24340589-A-G
• rs3212247

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 0.126 in 152,190 control chromosomes in the GnomAD database, including 1,610 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 0.13 (1610 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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: 0.126 AC: 19135 AN: 152072 Hom.: 1602 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.126 AC: 19172 AN: 152190 Hom.: 1610 Cov.: 33 AF XY: 0.131 AC XY: 9785 AN XY: 74414

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0915

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0834 Hom.: 877

Bravo AF: 0.124

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3212247; hg19: chr14-24809795;