14-78140481-A-G

Variant names:

• chr14-78140481-A-G
• rs888412

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 0.781 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.870 AC: 36108 AN: 41512

American (AMR) AF: 0.841 AC: 12838 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2392 AN: 3466

East Asian (EAS) AF: 0.663 AC: 3420 AN: 5162

South Asian (SAS) AF: 0.863 AC: 4144 AN: 4804

European-Finnish (FIN) AF: 0.669 AC: 7047 AN: 10538

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50264 AN: 67962

Other (OTH) AF: 0.800 AC: 1683 AN: 2104

Alfa AF: 0.762 Hom.: 142970

Bravo AF: 0.797

Asia WGS AF: 0.812 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.24
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs888412; hg19: chr14-78606824;