19-23463609-G-A

Variant names:

• chr19-23463609-G-A
• rs584460

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 0.475 in 151,960 control chromosomes in the GnomAD database, including 18,134 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 0.48 (18134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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: 0.475 AC: 72101 AN: 151842 Hom.: 18098 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.475 AC: 72185 AN: 151960 Hom.: 18134 Cov.: 32 AF XY: 0.477 AC XY: 35463 AN XY: 74280

African (AFR) AF: 0.599 AC: 24820 AN: 41418

American (AMR) AF: 0.486 AC: 7434 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3466

East Asian (EAS) AF: 0.833 AC: 4294 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2151 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4255 AN: 10564

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26497 AN: 67936

Other (OTH) AF: 0.430 AC: 910 AN: 2114

Alfa AF: 0.404 Hom.: 4082

Bravo AF: 0.487

Asia WGS AF: 0.596 AC: 2073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs584460; hg19: chr19-23646411;