rs1951366

chr14-59881557-G-A

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 0.42 in 152,008 control chromosomes in the GnomAD database, including 14,310 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 0.42 (14310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.420 AC: 63778 AN: 151890 Hom.: 14281 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.420 AC: 63867 AN: 152008 Hom.: 14310 Cov.: 32 AF XY: 0.420 AC XY: 31206 AN XY: 74302

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.454

Alfa AF: 0.394 Hom.: 2471

Bravo AF: 0.433

Asia WGS AF: 0.598 AC: 2075 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	1.5
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951366; hg19: chr14-60348275;