19-3579483-C-T

Variant names:

• chr19-3579483-C-T
• rs12460403

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 0.116 in 152,150 control chromosomes in the GnomAD database, including 1,191 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 0.12 (1191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.116 AC: 17655 AN: 152032 Hom.: 1168 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.116 AC: 17718 AN: 152150 Hom.: 1191 Cov.: 32 AF XY: 0.115 AC XY: 8573 AN XY: 74388

African (AFR) AF: 0.178 AC: 7386 AN: 41506

American (AMR) AF: 0.114 AC: 1744 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5164

South Asian (SAS) AF: 0.0474 AC: 229 AN: 4828

European-Finnish (FIN) AF: 0.0847 AC: 898 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5870 AN: 68008

Other (OTH) AF: 0.0855 AC: 181 AN: 2116

Alfa AF: 0.0995 Hom.: 1609

Bravo AF: 0.125

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.54
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs12460403; hg19: chr19-3579481;