chr3-30602723-G-A

Variant names:

• chr3-30602723-G-A
• rs6785358

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 0.839 in 152,208 control chromosomes in the GnomAD database, including 53,660 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 0.84 (53660 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 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: 0.839 AC: 127631 AN: 152090 Hom.: 53614 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.839 AC: 127736 AN: 152208 Hom.: 53660 Cov.: 33 AF XY: 0.840 AC XY: 62548 AN XY: 74432

African (AFR) AF: 0.876 AC: 36346 AN: 41508

American (AMR) AF: 0.861 AC: 13178 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4511 AN: 5182

South Asian (SAS) AF: 0.765 AC: 3693 AN: 4828

European-Finnish (FIN) AF: 0.873 AC: 9258 AN: 10606

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.812 AC: 55184 AN: 67994

Other (OTH) AF: 0.833 AC: 1762 AN: 2114

Alfa AF: 0.839 Hom.: 9041

Bravo AF: 0.843

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.37
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6785358; hg19: chr3-30644215;