14-27919151-G-A

Variant names:

• chr14-27919151-G-A
• rs8012040

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 0.538 in 151,762 control chromosomes in the GnomAD database, including 22,830 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 0.54 (22830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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: 0.539 AC: 81676 AN: 151644 Hom.: 22831 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.538 AC: 81705 AN: 151762 Hom.: 22830 Cov.: 32 AF XY: 0.543 AC XY: 40268 AN XY: 74128

African (AFR) AF: 0.426 AC: 17642 AN: 41402

American (AMR) AF: 0.455 AC: 6911 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3466

East Asian (EAS) AF: 0.866 AC: 4429 AN: 5116

South Asian (SAS) AF: 0.604 AC: 2912 AN: 4820

European-Finnish (FIN) AF: 0.658 AC: 6941 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39174 AN: 67912

Other (OTH) AF: 0.524 AC: 1103 AN: 2104

Alfa AF: 0.549 Hom.: 64132

Bravo AF: 0.519

Asia WGS AF: 0.670 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs8012040; hg19: chr14-28388357;