rs1402516

chr14-47997332-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;