rs12893484

Variant names:

• chr14-53948020-G-A
• rs12893484

Your query was ambiguous. Multiple possible variants found:

• chr14-53948020-G-A
• chr14-53948020-G-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 0.43 in 151,836 control chromosomes in the GnomAD database, including 15,969 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 0.43 (15969 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.431 AC: 65320 AN: 151718 Hom.: 15962 Cov.: 30

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65342 AN: 151836 Hom.: 15969 Cov.: 30 AF XY: 0.428 AC XY: 31756 AN XY: 74184

African (AFR) AF: 0.231 AC: 9554 AN: 41398

American (AMR) AF: 0.343 AC: 5231 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1326 AN: 5134

South Asian (SAS) AF: 0.318 AC: 1528 AN: 4800

European-Finnish (FIN) AF: 0.627 AC: 6606 AN: 10544

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38025 AN: 67938

Other (OTH) AF: 0.429 AC: 903 AN: 2104

Alfa AF: 0.512 Hom.: 14284

Bravo AF: 0.403

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.64
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs12893484; hg19: chr14-54414738; COSMIC: COSV55417150;