3-30694856-A-G

Variant names:

• chr3-30694856-A-G
• rs1461085

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 0.227 in 152,080 control chromosomes in the GnomAD database, including 4,781 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 0.23 (4781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.227 AC: 34464 AN: 151962 Hom.: 4785 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.227 AC: 34448 AN: 152080 Hom.: 4781 Cov.: 32 AF XY: 0.227 AC XY: 16901 AN XY: 74330

African (AFR) AF: 0.0937 AC: 3891 AN: 41506

American (AMR) AF: 0.151 AC: 2310 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3468

East Asian (EAS) AF: 0.0944 AC: 487 AN: 5160

South Asian (SAS) AF: 0.171 AC: 822 AN: 4818

European-Finnish (FIN) AF: 0.397 AC: 4196 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21487 AN: 67966

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.158 Hom.: 349

Bravo AF: 0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1461085; hg19: chr3-30736348;