rs1270884

chr12-114247766-A-G

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 0.625 in 152,090 control chromosomes in the GnomAD database, including 30,938 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 0.62 (30938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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: 0.624 AC: 94895 AN: 151972 Hom.: 30879 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.625 AC: 95011 AN: 152090 Hom.: 30938 Cov.: 32 AF XY: 0.626 AC XY: 46521 AN XY: 74316

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.613

Alfa AF: 0.549 Hom.: 5716

Bravo AF: 0.641

Asia WGS AF: 0.701 AC: 2436 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	0.20
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1270884; hg19: chr12-114685571;