rs1476470

Positions:

• chr12-110829227-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.53 in 151,762 control chromosomes in the GnomAD database, including 21,965 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 0.53 (21965 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80283 AN: 151644 Hom.: 21945 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.530 AC: 80360 AN: 151762 Hom.: 21965 Cov.: 30 AF XY: 0.528 AC XY: 39161 AN XY: 74116

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.532

Alfa AF: 0.505 Hom.: 8991

Bravo AF: 0.538

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476470; hg19: chr12-111267031;