rs1584930

Variant names:

• chr3-94243015-A-G
• rs1584930

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 0.157 in 152,132 control chromosomes in the GnomAD database, including 2,047 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 0.16 (2047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.157 AC: 23856 AN: 152016 Hom.: 2033 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.157 AC: 23899 AN: 152132 Hom.: 2047 Cov.: 32 AF XY: 0.156 AC XY: 11585 AN XY: 74392

African (AFR) AF: 0.224 AC: 9292 AN: 41482

American (AMR) AF: 0.135 AC: 2069 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3470

East Asian (EAS) AF: 0.158 AC: 815 AN: 5166

South Asian (SAS) AF: 0.125 AC: 602 AN: 4814

European-Finnish (FIN) AF: 0.109 AC: 1159 AN: 10600

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8814 AN: 68000

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.142 Hom.: 880

Bravo AF: 0.162

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.017
DANN	Benign	0.47
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1584930; hg19: chr3-93961859;