3-1028355-A-G

Variant names:

• chr3-1028355-A-G
• rs17032482

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 0.384 in 151,790 control chromosomes in the GnomAD database, including 11,677 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 0.38 (11677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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: 0.384 AC: 58219 AN: 151672 Hom.: 11670 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.384 AC: 58260 AN: 151790 Hom.: 11677 Cov.: 32 AF XY: 0.381 AC XY: 28226 AN XY: 74172

African (AFR) AF: 0.378 AC: 15648 AN: 41438

American (AMR) AF: 0.305 AC: 4646 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3466

East Asian (EAS) AF: 0.0807 AC: 417 AN: 5166

South Asian (SAS) AF: 0.302 AC: 1458 AN: 4826

European-Finnish (FIN) AF: 0.420 AC: 4434 AN: 10548

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29023 AN: 67778

Other (OTH) AF: 0.384 AC: 810 AN: 2112

Alfa AF: 0.405 Hom.: 21469

Bravo AF: 0.374

Asia WGS AF: 0.184 AC: 641 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17032482; hg19: chr3-1070039;