rs8016079

Positions:

• chr14-92292101-G-A

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 0.115 in 152,206 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.92292101G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17450 AN: 152086 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.115 AC: 17462 AN: 152206 Hom.: 1073 Cov.: 32 AF XY: 0.116 AC XY: 8651 AN XY: 74412

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.124

Alfa AF: 0.123 Hom.: 743

Bravo AF: 0.117

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8016079; hg19: chr14-92758445;