rs1991391

Variant names:

• chr12-114914861-G-A
• rs1991391

Your query was ambiguous. Multiple possible variants found:

• chr12-114914861-G-A
• chr12-114914861-G-C
• chr12-114914861-G-T

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 0.347 in 151,912 control chromosomes in the GnomAD database, including 9,530 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 0.35 (9530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.347 AC: 52745 AN: 151796 Hom.: 9523 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.347 AC: 52788 AN: 151912 Hom.: 9530 Cov.: 31 AF XY: 0.343 AC XY: 25441 AN XY: 74232

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.363

Alfa AF: 0.335 Hom.: 1550

Bravo AF: 0.347

Asia WGS AF: 0.249 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.036
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991391; hg19: chr12-115352666;