19-30089690-A-G

Variant names:

• chr19-30089690-A-G
• rs440675

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 0.0553 in 152,326 control chromosomes in the GnomAD database, including 280 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 0.055 (280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0647 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: 0.0553 AC: 8418 AN: 152208 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0553 AC: 8427 AN: 152326 Hom.: 280 Cov.: 33 AF XY: 0.0523 AC XY: 3894 AN XY: 74498

African (AFR) AF: 0.0667 AC: 2774 AN: 41570

American (AMR) AF: 0.0538 AC: 824 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0812 AC: 282 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5178

South Asian (SAS) AF: 0.0435 AC: 210 AN: 4826

European-Finnish (FIN) AF: 0.0113 AC: 120 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4031 AN: 68034

Other (OTH) AF: 0.0591 AC: 125 AN: 2116

Alfa AF: 0.0604 Hom.: 498

Bravo AF: 0.0592

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.23
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs440675; hg19: chr19-30580597;