rs720390

Variant names:

• chr3-185830895-G-A
• rs720390

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 0.374 in 152,056 control chromosomes in the GnomAD database, including 10,802 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 0.37 (10802 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.373 AC: 56728 AN: 151938 Hom.: 10776 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.374 AC: 56797 AN: 152056 Hom.: 10802 Cov.: 32 AF XY: 0.371 AC XY: 27565 AN XY: 74330

African (AFR) AF: 0.404 AC: 16749 AN: 41460

American (AMR) AF: 0.274 AC: 4194 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1542 AN: 3472

East Asian (EAS) AF: 0.168 AC: 871 AN: 5182

South Asian (SAS) AF: 0.309 AC: 1488 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4379 AN: 10560

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26135 AN: 67964

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.367 Hom.: 35707

Bravo AF: 0.362

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs720390; hg19: chr3-185548683;