rs12587990

Variant names:

• chr14-83718194-C-A
• rs12587990

Your query was ambiguous. Multiple possible variants found:

• chr14-83718194-C-A
• chr14-83718194-C-G
• chr14-83718194-C-T

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 0.181 in 152,054 control chromosomes in the GnomAD database, including 2,976 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 0.18 (2976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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: 0.181 AC: 27494 AN: 151936 Hom.: 2976 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.181 AC: 27504 AN: 152054 Hom.: 2976 Cov.: 32 AF XY: 0.184 AC XY: 13668 AN XY: 74348

African (AFR) AF: 0.113 AC: 4674 AN: 41504

American (AMR) AF: 0.215 AC: 3273 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3466

East Asian (EAS) AF: 0.506 AC: 2607 AN: 5148

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4818

European-Finnish (FIN) AF: 0.180 AC: 1900 AN: 10574

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12348 AN: 67978

Other (OTH) AF: 0.185 AC: 391 AN: 2112

Alfa AF: 0.123 Hom.: 288

Bravo AF: 0.185

Asia WGS AF: 0.377 AC: 1308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.067
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12587990; hg19: chr14-84184538;