rs1878321

Variant names:

• chr2-112786857-A-G
• rs1878321

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 0.322 in 151,960 control chromosomes in the GnomAD database, including 8,221 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 0.32 (8221 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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 (AFR) allele frequency at 95% confidence interval = 0.402 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: 0.321 AC: 48813 AN: 151842 Hom.: 8204 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.322 AC: 48874 AN: 151960 Hom.: 8221 Cov.: 31 AF XY: 0.321 AC XY: 23842 AN XY: 74280

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.309

Alfa AF: 0.326 Hom.: 1419

Bravo AF: 0.321

Asia WGS AF: 0.214 AC: 748 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	1.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878321; hg19: chr2-113544434;