rs8012040

chr14-27919151-G-Achr14-27919151-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 0.538 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.524

Alfa AF: 0.557 Hom.: 39133

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8012040; hg19: chr14-28388357;