rs1476470

Variant names:

• chr12-110829227-C-T
• rs1476470

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.624 AC: 25787 AN: 41358

American (AMR) AF: 0.612 AC: 9320 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1166 AN: 5158

South Asian (SAS) AF: 0.570 AC: 2744 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5212 AN: 10502

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33182 AN: 67918

Other (OTH) AF: 0.532 AC: 1120 AN: 2104

Alfa AF: 0.502 Hom.: 9888

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1476470; hg19: chr12-111267031;