rs12414884

Variant names:

• chr10-5021206-T-G
• rs12414884

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 0.43 in 152,080 control chromosomes in the GnomAD database, including 14,837 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 0.43 (14837 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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: 0.431 AC: 65428 AN: 151962 Hom.: 14831 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65463 AN: 152080 Hom.: 14837 Cov.: 31 AF XY: 0.432 AC XY: 32092 AN XY: 74346

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.428

Alfa AF: 0.477 Hom.: 12440

Bravo AF: 0.428

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12414884; hg19: chr10-5063398;