14-78140481-A-G

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 0.781 in 152,018 control chromosomes in the GnomAD database, including 46,715 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 0.78 (46715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.781 AC: 118608 AN: 151900 Hom.: 46661 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.781 AC: 118723 AN: 152018 Hom.: 46715 Cov.: 31 AF XY: 0.779 AC XY: 57857 AN XY: 74282

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.800

Alfa AF: 0.754 Hom.: 89085

Bravo AF: 0.797

Asia WGS AF: 0.812 AC: 2823 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	0.35
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888412; hg19: chr14-78606824;