14-86584462-A-G

Variant names:

• chr14-86584462-A-G
• rs1959305

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.128 in 152,102 control chromosomes in the GnomAD database, including 1,810 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 0.13 (1810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19527 AN: 151984 Hom.: 1809 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.128 AC: 19535 AN: 152102 Hom.: 1810 Cov.: 32 AF XY: 0.135 AC XY: 10053 AN XY: 74328

African (AFR) AF: 0.0765 AC: 3175 AN: 41526

American (AMR) AF: 0.145 AC: 2211 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2718 AN: 5144

South Asian (SAS) AF: 0.156 AC: 751 AN: 4818

European-Finnish (FIN) AF: 0.200 AC: 2120 AN: 10584

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7858 AN: 67966

Other (OTH) AF: 0.112 AC: 236 AN: 2116

Alfa AF: 0.110 Hom.: 1610

Bravo AF: 0.125

Asia WGS AF: 0.295 AC: 1023 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	2.2
DANN	Benign	0.65
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1959305; hg19: chr14-87050806;