3-30291356-C-A

Variant names:

• chr3-30291356-C-A
• rs17081352

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 0.0611 in 152,236 control chromosomes in the GnomAD database, including 348 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 0.061 (348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 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 = 0.0906 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: 0.0611 AC: 9290 AN: 152118 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0611 AC: 9300 AN: 152236 Hom.: 348 Cov.: 32 AF XY: 0.0629 AC XY: 4682 AN XY: 74442

African (AFR) AF: 0.0930 AC: 3863 AN: 41528

American (AMR) AF: 0.0493 AC: 754 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4828

European-Finnish (FIN) AF: 0.0895 AC: 949 AN: 10602

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2893 AN: 68020

Other (OTH) AF: 0.0678 AC: 143 AN: 2110

Alfa AF: 0.0317 Hom.: 37

Bravo AF: 0.0601

Asia WGS AF: 0.0410 AC: 144 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	3.3
DANN	Benign	0.50
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs17081352; hg19: chr3-30332847;