chr14-87039904-A-T

Position:

• chr14-87039904-A-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 0.0806 in 152,062 control chromosomes in the GnomAD database, including 697 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 0.081 (697 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.87039904A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12260 AN: 151944 Hom.: 698 Cov.: 31

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0806 AC: 12257 AN: 152062 Hom.: 697 Cov.: 31 AF XY: 0.0791 AC XY: 5881 AN XY: 74312

Gnomad4 AFR AF: 0.0237

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.0119

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0961

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0214 Hom.: 100

Bravo AF: 0.0724

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11624056; hg19: chr14-87506248;