rs379999

Positions:

• chr14-56056788-T-C

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/exons	MANE	UniProt

Ensembl

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