rs1951366

Variant names:

• chr14-59881557-G-A
• rs1951366

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;