rs184583

Variant names:

• chr19-29880683-T-A
• rs184583

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 0.0739 in 152,320 control chromosomes in the GnomAD database, including 594 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 0.074 (594 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 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: 0.0739 AC: 11251 AN: 152202 Hom.: 593 Cov.: 33

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0739 AC: 11258 AN: 152320 Hom.: 594 Cov.: 33 AF XY: 0.0796 AC XY: 5931 AN XY: 74496

African (AFR) AF: 0.0546 AC: 2268 AN: 41570

American (AMR) AF: 0.158 AC: 2411 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0658 AC: 342 AN: 5196

South Asian (SAS) AF: 0.196 AC: 949 AN: 4830

European-Finnish (FIN) AF: 0.0725 AC: 770 AN: 10622

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

European-Non Finnish (NFE) AF: 0.0609 AC: 4142 AN: 68022

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0642 Hom.: 33

Bravo AF: 0.0773

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs184583; hg19: chr19-30371590;