chr14-87702658-A-G

Position:

• chr14-87702658-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 0.934 in 152,196 control chromosomes in the GnomAD database, including 66,778 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 0.93 (66778 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.87702658A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142055 AN: 152078 Hom.: 66746 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.934 AC: 142142 AN: 152196 Hom.: 66778 Cov.: 31 AF XY: 0.936 AC XY: 69619 AN XY: 74406

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.967

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.939

Alfa AF: 0.969 Hom.: 27160

Bravo AF: 0.926

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899920; hg19: chr14-88169002;