rs1877780

Variant names:

• chr12-101224019-G-A
• rs1877780

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.678 in 152,072 control chromosomes in the GnomAD database, including 35,539 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 0.68 (35539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.678 AC: 103012 AN: 151954 Hom.: 35490 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.678 AC: 103116 AN: 152072 Hom.: 35539 Cov.: 32 AF XY: 0.685 AC XY: 50909 AN XY: 74326

African (AFR) AF: 0.787 AC: 32653 AN: 41504

American (AMR) AF: 0.662 AC: 10104 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4166 AN: 5162

South Asian (SAS) AF: 0.731 AC: 3523 AN: 4820

European-Finnish (FIN) AF: 0.723 AC: 7646 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40722 AN: 67964

Other (OTH) AF: 0.661 AC: 1396 AN: 2112

Alfa AF: 0.625 Hom.: 111649

Bravo AF: 0.680

Asia WGS AF: 0.783 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1877780; hg19: chr12-101617797;