rs379820

Variant names:

• chr3-13444158-A-G
• rs379820

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 0.654 in 151,992 control chromosomes in the GnomAD database, including 33,758 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 0.65 (33758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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: 0.654 AC: 99255 AN: 151874 Hom.: 33705 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.654 AC: 99373 AN: 151992 Hom.: 33758 Cov.: 32 AF XY: 0.648 AC XY: 48147 AN XY: 74298

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.663

Alfa AF: 0.634 Hom.: 3902

Bravo AF: 0.662

Asia WGS AF: 0.529 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379820; hg19: chr3-13485658;