12-10455414-G-C

Variant names:

• chr12-10455414-G-C
• rs1983526

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 0.363 in 151,772 control chromosomes in the GnomAD database, including 11,051 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 0.36 (11051 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 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: 0.363 AC: 55075 AN: 151654 Hom.: 11043 Cov.: 30

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.363 AC: 55100 AN: 151772 Hom.: 11051 Cov.: 30 AF XY: 0.368 AC XY: 27297 AN XY: 74168

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.374

Alfa AF: 0.378 Hom.: 1418

Bravo AF: 0.355

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
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: rs1983526; hg19: chr12-10608013;