rs871880

Variant names:

• chr12-43331201-A-T
• rs871880

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 0.493 in 151,850 control chromosomes in the GnomAD database, including 19,199 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 0.49 (19199 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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: 0.493 AC: 74775 AN: 151732 Hom.: 19179 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.493 AC: 74847 AN: 151850 Hom.: 19199 Cov.: 31 AF XY: 0.498 AC XY: 36999 AN XY: 74226

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.529

Alfa AF: 0.454 Hom.: 1991

Bravo AF: 0.507

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs871880; hg19: chr12-43725004;