12-65976791-C-T

Variant names:

• chr12-65976791-C-T
• rs1480464

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 0.208 in 152,068 control chromosomes in the GnomAD database, including 4,440 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 0.21 (4440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.209 AC: 31694 AN: 151950 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152068 Hom.: 4440 Cov.: 32 AF XY: 0.213 AC XY: 15844 AN XY: 74344

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.215

Alfa AF: 0.206 Hom.: 1935

Bravo AF: 0.222

Asia WGS AF: 0.459 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1480464; hg19: chr12-66370571;