3-119688556-A-G

Variant names:

• chr3-119688556-A-G
• rs2137619

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 0.305 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.190 AC: 7899 AN: 41512

American (AMR) AF: 0.377 AC: 5754 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1251 AN: 5180

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4826

European-Finnish (FIN) AF: 0.419 AC: 4426 AN: 10570

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23647 AN: 67964

Other (OTH) AF: 0.327 AC: 691 AN: 2114

Alfa AF: 0.335 Hom.: 14709

Bravo AF: 0.301

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.57
DANN	Benign	0.55
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2137619; hg19: chr3-119407403;