rs12414884

Variant names:

• chr10-5021206-T-G
• rs12414884

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.316 AC: 13101 AN: 41476

American (AMR) AF: 0.528 AC: 8069 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1464 AN: 3466

East Asian (EAS) AF: 0.191 AC: 989 AN: 5170

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5721 AN: 10580

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33058 AN: 67968

Other (OTH) AF: 0.428 AC: 904 AN: 2112

Alfa AF: 0.462 Hom.: 19581

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12414884; hg19: chr10-5063398;