14-104798626-A-G

Position:

• chr14-104798626-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 0.844 in 152,188 control chromosomes in the GnomAD database, including 55,385 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 0.84 (55385 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.104798626A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128399 AN: 152070 Hom.: 55341 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.844 AC: 128508 AN: 152188 Hom.: 55385 Cov.: 33 AF XY: 0.837 AC XY: 62328 AN XY: 74422

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.845

Alfa AF: 0.882 Hom.: 8660

Bravo AF: 0.832

Asia WGS AF: 0.515 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2498784; hg19: chr14-105264963;