rs379999

Variant names:

• chr14-56056788-T-C
• rs379999

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 0.0755 in 152,258 control chromosomes in the GnomAD database, including 786 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 0.076 (786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 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: 0.0756 AC: 11499 AN: 152140 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0755 AC: 11501 AN: 152258 Hom.: 786 Cov.: 32 AF XY: 0.0770 AC XY: 5733 AN XY: 74444

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0428 Hom.: 620

Bravo AF: 0.0776

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379999; hg19: chr14-56523506;