3-119688556-A-G

Variant names:

• chr3-119688556-A-G
• rs2137619

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 0.305 in 152,110 control chromosomes in the GnomAD database, including 7,626 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 0.31 (7626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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: 0.305 AC: 46382 AN: 151992 Hom.: 7616 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.305 AC: 46412 AN: 152110 Hom.: 7626 Cov.: 32 AF XY: 0.308 AC XY: 22912 AN XY: 74374

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.327

Alfa AF: 0.339 Hom.: 11771

Bravo AF: 0.301

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.57
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137619; hg19: chr3-119407403;