14-83001870-A-G

Position:

• chr14-83001870-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 0.0768 in 152,242 control chromosomes in the GnomAD database, including 548 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 0.077 (548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0769 AC: 11693 AN: 152124 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0768 AC: 11686 AN: 152242 Hom.: 548 Cov.: 32 AF XY: 0.0777 AC XY: 5783 AN XY: 74438

Gnomad4 AFR AF: 0.0349

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0908 Hom.: 422

Bravo AF: 0.0700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2022767; hg19: chr14-83468214;