rs379820

Variant names:

• chr3-13444158-A-G
• rs379820

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.845 AC: 35066 AN: 41492

American (AMR) AF: 0.524 AC: 7994 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2312 AN: 5180

South Asian (SAS) AF: 0.518 AC: 2494 AN: 4818

European-Finnish (FIN) AF: 0.539 AC: 5660 AN: 10492

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41305 AN: 67960

Other (OTH) AF: 0.663 AC: 1397 AN: 2108

Alfa AF: 0.642 Hom.: 4176

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs379820; hg19: chr3-13485658;