rs1402516

Variant names:

• chr14-47997332-G-A
• rs1402516

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0431 in 152,196 control chromosomes in the GnomAD database, including 456 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 0.043 (456 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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: 0.0431 AC: 6558 AN: 152078 Hom.: 457 Cov.: 33

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0431 AC: 6560 AN: 152196 Hom.: 456 Cov.: 33 AF XY: 0.0457 AC XY: 3400 AN XY: 74414

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0228

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0310 Hom.: 15

Bravo AF: 0.0461

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
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: rs1402516; hg19: chr14-48466535;