rs4530059

Variant names:

• chr14-104302812-G-A
• rs4530059

Your query was ambiguous. Multiple possible variants found:

• chr14-104302812-G-A
• chr14-104302812-G-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 0.347 in 152,178 control chromosomes in the GnomAD database, including 9,284 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 0.35 (9284 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 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: 0.347 AC: 52776 AN: 152060 Hom.: 9285 Cov.: 34

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.347 AC: 52792 AN: 152178 Hom.: 9284 Cov.: 34 AF XY: 0.349 AC XY: 25934 AN XY: 74394

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.355

Alfa AF: 0.318 Hom.: 4050

Bravo AF: 0.351

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4530059; hg19: chr14-104769149;